diff --git a/HISTORY.TXT b/HISTORY.TXT index 5503a8cd..5e90a86b 100644 --- a/HISTORY.TXT +++ b/HISTORY.TXT @@ -42,7 +42,7 @@ List of changes from version 3.2 to 3.2.1 (until October 23rd, 2015) - comparative gene prediction (CGP): make the parameters from the GCB proceedings paper match again - new CGP default parameters (tested on 5 clades) - CGP version penalizes very long introns equivalently to a geometric distribution - - code now under artistic licence only + - code now under artistic license only List of changes from version 3.1 to 3.2 (until September 25th, 2015) - comparative gene prediction (CGP option) has sensible default parameters of the logistic regression model - new tool hal2maf_split.pl for splitting an alignment for parallel comparative prediction @@ -85,10 +85,10 @@ List of changes from version 3.0.2 to 3.0.3 (until August 28th, 2014) - other bugfixes in comparative mode - removal of mysql++ code from package: this is available as Debian/Ubuntu package List of changes from version 3.0 to 3.0.2 (until February 22nd, 2014) - - inclusion of scanner and parser code for Newick tree format (GPL licence), easier installation of + - inclusion of scanner and parser code for Newick tree format (GPL license), easier installation of comparative augustus functionality - - therefore release under more restrictive GPL licence (the plan is to replace this later - and switch back to the more permissive and non-viral artistic open source licence) + - therefore release under more restrictive GPL license (the plan is to replace this later + and switch back to the more permissive and non-viral artistic open source license) - drop requirement to set environment variable AUGUSTUS_CONFIG_PATH - bugfixes (etraining: "not Genbank format", gtf2gff.pl, compilation warning) List of changes from version 2.7 to 3.0 (until January 8th, 2014) @@ -153,7 +153,7 @@ List of changes from version 2.4 to 2.5 (until Nov 13th, 2010) - new species pneumocystis (fungus), user contributed by Marco Pagni List of changes from version 2.3.1 to 2.4 (until July 27, 2010) - improved human parameter set: roughly 13 percent points better on CDS exon level - - improved fly paramter set + - improved fly parameter set - added new species 'lamprey', contributed by Falk Hildebrand and Shigehiro Kuraku - added new species Leishmania tarentolae, Trichinella spiralis - added maize5 parameter set, better than 'maize' and with UTR model @@ -274,7 +274,7 @@ List of changes from version 1.6 to version 1.7 (until October 5th, 2005): List of changes from version 1.5 to version 1.6 (until August 3rd, 2005): - - The source code is now freely available (Artistic Licence). + - The source code is now freely available (Artistic License). - New species: Tribolium castaneum, Aedes aegypti, Coprinus cinereus - Bugfix: Wrong interpretation of reading frame for reverse strand exon hints. - Training of hints possible with nested genes. diff --git a/README-cgp.md b/README-cgp.md index 83273023..6dbb3742 100644 --- a/README-cgp.md +++ b/README-cgp.md @@ -10,7 +10,7 @@ (not needed unless you run into compiler errors related to 'parse.cc' or 'lex.cc') [AUTHORS AND CONTACT](docs/CONTACT.md) [REFERENCES](README.md#references) -[LICENCES](README.md#licenses) +[LICENSES](README.md#licenses) # INTRODUCTION diff --git a/README.md b/README.md index b9d614d4..bb571b10 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ [WEB-SERVER](#web-server) [AUTHORS AND CONTACT](docs/CONTACT.md) [REFERENCES](#references) -[LICENCES](#licenses) +[LICENSES](#licenses) # INTRODUCTION diff --git a/augustus-training/dynamic/about.html b/augustus-training/dynamic/about.html index a189cbbb..1b5e831c 100644 --- a/augustus-training/dynamic/about.html +++ b/augustus-training/dynamic/about.html @@ -35,7 +35,7 @@

Gene prediction with AUGUSTUS

with cDNA
Click on image to enlarge!

-
  • AUGUSTUS ususally belongs to the most accurate programs for the species it is trained +
  • AUGUSTUS usually belongs to the most accurate programs for the species it is trained for. Often it is the most accurate ab initio program. For example, at the independent gene finder assessment (EGASP) on the human ENCODE regions AUGUSTUS was the most accurate gene finder among the tested ab initio programs. At the more recent nGASP (worm), it was among the best in the ab initio @@ -67,7 +67,7 @@

    Gene prediction with AUGUSTUS

  • AUGUSTUS can report a large number of alternative genes, including probabilities for the transcripts and each exon and intron. You can make AUGUSTUS predict suboptimal gene structures (example) and you can adjust command line paramters to regulate +href="images/alternative-sampling.png">example) and you can adjust command line parameters to regulate the number of reported alternatives.
    • diff --git a/augustus-training/grails-app/views/about.gsp b/augustus-training/grails-app/views/about.gsp index 02bba6c6..1dbbe4c9 100644 --- a/augustus-training/grails-app/views/about.gsp +++ b/augustus-training/grails-app/views/about.gsp @@ -152,7 +152,7 @@
  • AUGUSTUS can report a large number of alternative genes, including probabilities for the transcripts and each exon and intron. You can make AUGUSTUS predict suboptimal gene structures (example) and you can adjust command line paramters to regulate + href="images/alternative-sampling.png">example) and you can adjust command line parameters to regulate the number of reported alternatives.
    • diff --git a/augustus-training/grails-app/views/help.gsp b/augustus-training/grails-app/views/help.gsp index 05aac5ec..da0c7d62 100644 --- a/augustus-training/grails-app/views/help.gsp +++ b/augustus-training/grails-app/views/help.gsp @@ -799,7 +799,7 @@ HS04636 anchor intronpart 7631 7633 0 + 0 source=M # Setting 1group1gene for E. # Sources of extrinsic information: M E # Have extrinsic information about 1 sequences (in the specified range). -# Initialising the parameters ... +# Initializing the parameters ... # human version. Use default transition matrix. # Looks like /var/tmp/augustus/AUG-1855139717/input.fa is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. diff --git a/augustus-training/grails-app/views/predictiontutorial.gsp b/augustus-training/grails-app/views/predictiontutorial.gsp index fc561662..58be2bcc 100644 --- a/augustus-training/grails-app/views/predictiontutorial.gsp +++ b/augustus-training/grails-app/views/predictiontutorial.gsp @@ -1065,7 +1065,7 @@ HS04636 anchor intronpart 7631 7633 0 + 0 source=M # Setting 1group1gene for E. # Sources of extrinsic information: M E # Have extrinsic information about 1 sequences (in the specified range). -# Initialising the parameters ... +# Initializing the parameters ... # human version. Use default transition matrix. # Looks like /var/tmp/augustus/AUG-1855139717/input.fa is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. diff --git a/augustus-training/plugins/plugins-list-default.xml b/augustus-training/plugins/plugins-list-default.xml index a919434b..bc548e82 100644 --- a/augustus-training/plugins/plugins-list-default.xml +++ b/augustus-training/plugins/plugins-list-default.xml @@ -31822,7 +31822,7 @@ It integrates nicely with the resources plugin. Git Plugin Peter Ledbrook p.ledbrook@cacoethes.co.uk - Integrates git, the distributed version control system, into Grails projects. It can initialise a local git repository for your project, add a .gitignore file and commit the first version of your source code. + Integrates git, the distributed version control system, into Grails projects. It can initialize a local git repository for your project, add a .gitignore file and commit the first version of your source code. http://plugins.grails.org/grails-git/tags/RELEASE_1_0-SNAPSHOT/grails-git-1.0-SNAPSHOT.zip diff --git a/auxprogs/bam2hints/bam2hints.cc b/auxprogs/bam2hints/bam2hints.cc index 1e730c0d..e3f6189c 100644 --- a/auxprogs/bam2hints/bam2hints.cc +++ b/auxprogs/bam2hints/bam2hints.cc @@ -820,7 +820,7 @@ int main(int argc, char* argv[]) // check if there is a proper old target if(OldTargetID >= 0) // -1 <-> "*"(unknown reference), -2 <-> uninitialized { - // check previous occurence of that target + // check previous occurrence of that target if(seenRefSet.find(TargetName) != seenRefSet.end()) { if(IntOnly && Mult) @@ -1069,7 +1069,7 @@ int main(int argc, char* argv[]) // TASK: else store alignment pointer into map // TASK: set new or reuse "pal" - } // end while (parsing through bam aligment lines) + } // end while (parsing through bam alignment lines) // newline after display of the line count diff --git a/auxprogs/bam2wig/bam2wig.c b/auxprogs/bam2wig/bam2wig.c index cce7c507..47912d9b 100644 --- a/auxprogs/bam2wig/bam2wig.c +++ b/auxprogs/bam2wig/bam2wig.c @@ -91,7 +91,7 @@ int main(int argc, char *argv[]) } - // Initialising auxiliary data structures + // Initializing auxiliary data structures data = calloc(1, sizeof(void*)); // data[0] is array for just one BAM file // set the default region. left-shift "end" by appending 30 zeros (i.e. end=1073741824) beg = 0; end = 1<<30; tid = -1; diff --git a/auxprogs/filterBam/src/filterBam.cc b/auxprogs/filterBam/src/filterBam.cc index 11f912b0..a577c5a6 100644 --- a/auxprogs/filterBam/src/filterBam.cc +++ b/auxprogs/filterBam/src/filterBam.cc @@ -149,7 +149,7 @@ int main(int argc, char *argv[]) optionalCounters.outPaired = outPaired; optionalCounters.outUniq = outUniq; optionalCounters.outBest = outBest; - // Initialising options + // Initializing options struct globalOptions_t globalOptions; globalOptions = initOptions(argc, argv); bool best = globalOptions.best; diff --git a/auxprogs/filterBam/src/functions/MatePairs.cc b/auxprogs/filterBam/src/functions/MatePairs.cc index f437d19d..4001dbf9 100644 --- a/auxprogs/filterBam/src/functions/MatePairs.cc +++ b/auxprogs/filterBam/src/functions/MatePairs.cc @@ -55,7 +55,7 @@ MatePairs::MatePairs(const MatePairs ©in) // Copy constructor to handle pa this->score = copyin.score; } -// Initialisation method +// Initialization method MatePairs::MatePairs(int it, int jit, float score) { this->alIt = it; @@ -63,7 +63,7 @@ MatePairs::MatePairs(int it, int jit, float score) this->score = score; } -// Initialisation method +// Initialization method void MatePairs::setValues(int it, int jit, float score) { this->alIt = it; diff --git a/auxprogs/filterBam/src/functions/PairednessCoverage.cc b/auxprogs/filterBam/src/functions/PairednessCoverage.cc index 2da2d1eb..a7eedf9f 100644 --- a/auxprogs/filterBam/src/functions/PairednessCoverage.cc +++ b/auxprogs/filterBam/src/functions/PairednessCoverage.cc @@ -51,7 +51,7 @@ PairednessCoverage::PairednessCoverage(const PairednessCoverage ©in) // Co this->chr = copyin.chr; } -// Initialisation method +// Initialization method PairednessCoverage::PairednessCoverage(int coord, int label, string chr) { this->coord = coord; @@ -60,7 +60,7 @@ PairednessCoverage::PairednessCoverage(int coord, int label, string chr) } -// Initialisation method +// Initialization method void PairednessCoverage::setValues(int coord, int label, string chr) { this->coord = coord; diff --git a/auxprogs/filterBam/src/functions/SingleAlignment.cc b/auxprogs/filterBam/src/functions/SingleAlignment.cc index a4d9b8ad..ccca4904 100644 --- a/auxprogs/filterBam/src/functions/SingleAlignment.cc +++ b/auxprogs/filterBam/src/functions/SingleAlignment.cc @@ -75,7 +75,7 @@ SingleAlignment::SingleAlignment(BamAlignment *al, float coverage, float percId, } -// Initialisation method +// Initialization method void SingleAlignment::setValues(BamAlignment *al, float coverage, float percId, const RefVector *refData) { this->al = al; diff --git a/auxprogs/filterBam/src/functions/initOptions.cc b/auxprogs/filterBam/src/functions/initOptions.cc index e6b86c7b..f9d64bc2 100644 --- a/auxprogs/filterBam/src/functions/initOptions.cc +++ b/auxprogs/filterBam/src/functions/initOptions.cc @@ -146,7 +146,7 @@ void displayUsage(int argc, char *argv[]) } -// Options initialisation +// Options initialization globalOptions_t initOptions(int argc, char *argv[]) { int opt = 0, longIndex; diff --git a/auxprogs/filterBam/src/headers/filterBam.h b/auxprogs/filterBam/src/headers/filterBam.h index 54c22746..616c2bdf 100644 --- a/auxprogs/filterBam/src/headers/filterBam.h +++ b/auxprogs/filterBam/src/headers/filterBam.h @@ -32,7 +32,7 @@ uint32_t sumMandIOperations(vector cigar, string printFlag); uint32_t sumDandIOperations(vector cigar, string printFlag); int printElapsedTime(int tEnd, int tStart); -// For option initialisation +// For option initialization struct globalOptions_t { bool best; bool help; diff --git a/auxprogs/homGeneMapping/include/bitmasking.hh b/auxprogs/homGeneMapping/include/bitmasking.hh index 096dd12e..535886bb 100644 --- a/auxprogs/homGeneMapping/include/bitmasking.hh +++ b/auxprogs/homGeneMapping/include/bitmasking.hh @@ -1,6 +1,6 @@ /********************************************************************** * file: bitmasking.hh - * licence: Artistic Licence, see file LICENCE.TXT or + * license: Artistic License, see file LICENSE.TXT or * http://www.opensource.org/licenses/artistic-license.php * descr.: usage of bit masks to pack multiple values into a single integer diff --git a/auxprogs/homGeneMapping/include/gene.hh b/auxprogs/homGeneMapping/include/gene.hh index 957c42ec..6032aaeb 100644 --- a/auxprogs/homGeneMapping/include/gene.hh +++ b/auxprogs/homGeneMapping/include/gene.hh @@ -1,6 +1,6 @@ /********************************************************************** * file: gene.hh - * licence: Artistic Licence, see file LICENCE.TXT or + * license: Artistic License, see file LICENSE.TXT or * http://www.opensource.org/licenses/artistic-license.php * descr.: * authors: Stefanie Koenig, stefaniekoenig@ymail.com diff --git a/auxprogs/homGeneMapping/include/genome.hh b/auxprogs/homGeneMapping/include/genome.hh index 11a9ccbf..b8e7f7fa 100644 --- a/auxprogs/homGeneMapping/include/genome.hh +++ b/auxprogs/homGeneMapping/include/genome.hh @@ -1,6 +1,6 @@ /********************************************************************** * file: genome.hh - * licence: Artistic Licence, see file LICENCE.TXT or + * license: Artistic License, see file LICENSE.TXT or * http://www.opensource.org/licenses/artistic-license.php * descr.: * authors: Stefanie Koenig, stefaniekoenig@ymail.com diff --git a/auxprogs/homGeneMapping/include/projectio.hh b/auxprogs/homGeneMapping/include/projectio.hh index fb2f54c3..d239f1ec 100644 --- a/auxprogs/homGeneMapping/include/projectio.hh +++ b/auxprogs/homGeneMapping/include/projectio.hh @@ -1,6 +1,6 @@ /********************************************************************** * file: projectio.hh - * licence: Artistic Licence, see file LICENCE.TXT or + * license: Artistic License, see file LICENSE.TXT or * http://www.opensource.org/licenses/artistic-license.php * descr.: * authors: Stefanie Koenig, stefaniekoenig@ymail.com @@ -69,7 +69,7 @@ inline std::string exec(const char* cmd) { */ inline std::string expandDir(std::string filename){ if(filename.length()>0 && filename[filename.size()-1] != '/') - filename += '/'; // append slash if neccessary + filename += '/'; // append slash if necessary filename = expandHome(filename); // replace "~" by "$HOME return filename; } diff --git a/auxprogs/homGeneMapping/include/sqliteDB.hh b/auxprogs/homGeneMapping/include/sqliteDB.hh index c165bb83..e842bcf9 100644 --- a/auxprogs/homGeneMapping/include/sqliteDB.hh +++ b/auxprogs/homGeneMapping/include/sqliteDB.hh @@ -1,6 +1,6 @@ /********************************************************************** * file: sqliteDB.hh - * licence: Artistic Licence, see file LICENCE.TXT or + * license: Artistic License, see file LICENSE.TXT or * http://www.opensource.org/licenses/artistic-license.php * descr.: wrapper class around the SQLite interface * authors: Stefanie Koenig diff --git a/auxprogs/homGeneMapping/src/gene.cc b/auxprogs/homGeneMapping/src/gene.cc index 4f381507..f521d92d 100644 --- a/auxprogs/homGeneMapping/src/gene.cc +++ b/auxprogs/homGeneMapping/src/gene.cc @@ -1,6 +1,6 @@ /********************************************************************** * file: gene.cc - * licence: Artistic Licence, see file LICENCE.TXT or + * license: Artistic License, see file LICENSE.TXT or * http://www.opensource.org/licenses/artistic-license.php * descr.: * authors: Stefanie Koenig, stefaniekoenig@ymail.com diff --git a/auxprogs/homGeneMapping/src/genome.cc b/auxprogs/homGeneMapping/src/genome.cc index 4cb4db57..7941089c 100644 --- a/auxprogs/homGeneMapping/src/genome.cc +++ b/auxprogs/homGeneMapping/src/genome.cc @@ -1,6 +1,6 @@ /********************************************************************** * file: genome.cc - * licence: Artistic Licence, see file LICENCE.TXT or + * license: Artistic License, see file LICENSE.TXT or * http://www.opensource.org/licenses/artistic-license.php * descr.: * authors: Stefanie Koenig, stefaniekoenig@ymail.com diff --git a/auxprogs/homGeneMapping/src/main.cc b/auxprogs/homGeneMapping/src/main.cc index 50f2a516..370d3ed6 100644 --- a/auxprogs/homGeneMapping/src/main.cc +++ b/auxprogs/homGeneMapping/src/main.cc @@ -1,6 +1,6 @@ /********************************************************************** * file: main.cc - * licence: Artistic Licence, see file LICENCE.TXT or + * license: Artistic License, see file LICENSE.TXT or * http://www.opensource.org/licenses/artistic-license.php * * authors: Stefanie Koenig diff --git a/auxprogs/homGeneMapping/src/sqliteDB.cc b/auxprogs/homGeneMapping/src/sqliteDB.cc index 8ffebb7a..95b51ff3 100644 --- a/auxprogs/homGeneMapping/src/sqliteDB.cc +++ b/auxprogs/homGeneMapping/src/sqliteDB.cc @@ -1,6 +1,6 @@ /********************************************************************** * file: sqliteDB.cc - * licence: Artistic Licence, see file LICENCE.TXT or + * license: Artistic License, see file LICENSE.TXT or * http://www.opensource.org/licenses/artistic-license.php * descr.: wrapper class around the SQLite interface * authors: Stefanie Koenig diff --git a/config/model/constraints_shadow_partial.txt b/config/model/constraints_shadow_partial.txt index 954efee9..1d42f643 100644 --- a/config/model/constraints_shadow_partial.txt +++ b/config/model/constraints_shadow_partial.txt @@ -51,7 +51,7 @@ # This section is for seting constraints between transition probabilities, # such as suggested by symmetry such as strand symmetry (or by treating transitions in # all reading frames the same). Theoretically, i.e. with infinite and -# representative traininig data, this should not be neccessary. However, in the real finite +# representative traininig data, this should not be necessary. However, in the real finite # world this is a little safeguard against overfitting. # [BINDINGS] diff --git a/config/model/constraints_shadow_partial_utr.txt b/config/model/constraints_shadow_partial_utr.txt index 7bdcc593..08cd3f41 100644 --- a/config/model/constraints_shadow_partial_utr.txt +++ b/config/model/constraints_shadow_partial_utr.txt @@ -63,10 +63,10 @@ 32 36 # -------------------------------------------------------------------- -# This section is for seting constraints between transition probabilities, +# This section is for setting constraints between transition probabilities, # such as suggested by symmetry such as strand symmetry (or by treating transitions in # all reading frames the same). Theoretically, i.e. with infinite and -# representative traininig data, this should not be neccessary. However, in the real finite +# representative training data, this should not be necessary. However, in the real finite # world this is a little safeguard against overfitting. # [BINDINGS] diff --git a/config/model/trans_shadow_atleastone.pbl b/config/model/trans_shadow_atleastone.pbl index bfd1a7bd..80f399db 100644 --- a/config/model/trans_shadow_atleastone.pbl +++ b/config/model/trans_shadow_atleastone.pbl @@ -8,7 +8,7 @@ # Date: 19.05.2003 # Initial probabilities (a priori probs for a state ending at a -# certain position, e.g. the position before the first nukleotide in +# certain position, e.g. the position before the first nucleotide in # the sequence or the last position. # only non-zero probabilities [Initial] @@ -20,7 +20,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 1 diff --git a/config/model/trans_shadow_bacterium.pbl b/config/model/trans_shadow_bacterium.pbl index 05f759fe..768690a3 100644 --- a/config/model/trans_shadow_bacterium.pbl +++ b/config/model/trans_shadow_bacterium.pbl @@ -21,7 +21,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 3 diff --git a/config/model/trans_shadow_complete.pbl b/config/model/trans_shadow_complete.pbl index c4ec5f92..3be69b16 100644 --- a/config/model/trans_shadow_complete.pbl +++ b/config/model/trans_shadow_complete.pbl @@ -8,7 +8,7 @@ # Date: 19.05.2003 # Initial probabilities (a priori probs for a state ending at a -# certain position, e.g. the position before the first nukleotide in +# certain position, e.g. the position before the first nucleotide in # the sequence or the last position. # only non-zero probabilities [Initial] @@ -20,7 +20,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 1 diff --git a/config/model/trans_shadow_complete_utr.pbl b/config/model/trans_shadow_complete_utr.pbl index 6b7fd88a..9df8fd71 100644 --- a/config/model/trans_shadow_complete_utr.pbl +++ b/config/model/trans_shadow_complete_utr.pbl @@ -18,7 +18,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 1 diff --git a/config/model/trans_shadow_exactlyone.pbl b/config/model/trans_shadow_exactlyone.pbl index 848988a0..ba49c1a6 100644 --- a/config/model/trans_shadow_exactlyone.pbl +++ b/config/model/trans_shadow_exactlyone.pbl @@ -8,7 +8,7 @@ # Date: 19.05.2003 # Initial probabilities (a priori probs for a state ending at a -# certain position, e.g. the position before the first nukleotide in +# certain position, e.g. the position before the first nucleotide in # the sequence or the last position. # only non-zero probabilities [Initial] @@ -20,7 +20,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 1 diff --git a/config/model/trans_shadow_intronless.pbl b/config/model/trans_shadow_intronless.pbl index 2247bd3a..6a9a0aeb 100644 --- a/config/model/trans_shadow_intronless.pbl +++ b/config/model/trans_shadow_intronless.pbl @@ -21,7 +21,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 3 diff --git a/config/model/trans_shadow_partial.pbl b/config/model/trans_shadow_partial.pbl index b4977f86..f8adba4e 100644 --- a/config/model/trans_shadow_partial.pbl +++ b/config/model/trans_shadow_partial.pbl @@ -67,7 +67,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 47 diff --git a/config/model/trans_shadow_partial_utr.pbl b/config/model/trans_shadow_partial_utr.pbl index c43a8292..b765d516 100644 --- a/config/model/trans_shadow_partial_utr.pbl +++ b/config/model/trans_shadow_partial_utr.pbl @@ -90,7 +90,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 71 diff --git a/config/model/trans_shadow_partial_utr_nc.pbl b/config/model/trans_shadow_partial_utr_nc.pbl index eb6a4f90..6ecf6dd4 100644 --- a/config/model/trans_shadow_partial_utr_nc.pbl +++ b/config/model/trans_shadow_partial_utr_nc.pbl @@ -100,7 +100,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 83 diff --git a/config/model/trans_singlestrand_atleastone.pbl b/config/model/trans_singlestrand_atleastone.pbl index 743d84ad..da5d8a7b 100644 --- a/config/model/trans_singlestrand_atleastone.pbl +++ b/config/model/trans_singlestrand_atleastone.pbl @@ -8,7 +8,7 @@ # Date: 19.05.2003 # Initial probabilities (a priori probs for a state ending at a -# certain position, e.g. the position before the first nukleotide in +# certain position, e.g. the position before the first nucleotide in # the sequence or the last position. # only non-zero probabilities [Initial] @@ -19,7 +19,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 1 diff --git a/config/model/trans_singlestrand_complete.pbl b/config/model/trans_singlestrand_complete.pbl index 3e65a3da..e674c575 100644 --- a/config/model/trans_singlestrand_complete.pbl +++ b/config/model/trans_singlestrand_complete.pbl @@ -8,7 +8,7 @@ # Date: 19.05.2003 # Initial probabilities (a priori probs for a state ending at a -# certain position, e.g. the position before the first nukleotide in +# certain position, e.g. the position before the first nucleotide in # the sequence or the last position. # only non-zero probabilities [Initial] @@ -19,7 +19,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 1 diff --git a/config/model/trans_singlestrand_exactlyone.pbl b/config/model/trans_singlestrand_exactlyone.pbl index 6a2c0ee2..088ac45a 100644 --- a/config/model/trans_singlestrand_exactlyone.pbl +++ b/config/model/trans_singlestrand_exactlyone.pbl @@ -8,7 +8,7 @@ # Date: 19.05.2003 # Initial probabilities (a priori probs for a state ending at a -# certain position, e.g. the position before the first nukleotide in +# certain position, e.g. the position before the first nucleotide in # the sequence or the last position. # only non-zero probabilities [Initial] @@ -19,7 +19,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 1 diff --git a/config/model/trans_singlestrand_partial.pbl b/config/model/trans_singlestrand_partial.pbl index 021d8e0f..4941a500 100644 --- a/config/model/trans_singlestrand_partial.pbl +++ b/config/model/trans_singlestrand_partial.pbl @@ -8,7 +8,7 @@ # Date: 19.05.2003 # Initial probabilities (a priori probs for a state ending at a -# certain position, e.g. the position before the first nukleotide in +# certain position, e.g. the position before the first nucleotide in # the sequence or the last position. # only non-zero probabilities [Initial] @@ -43,7 +43,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 24 diff --git a/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg b/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg index a2d75908..3755f672 100644 --- a/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg +++ b/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.134 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile Conidiobolus_coronatus_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile Conidiobolus_coronatus_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/E_coli_K12/E_coli_K12_parameters.cfg b/config/species/E_coli_K12/E_coli_K12_parameters.cfg index 1217e858..394312b1 100644 --- a/config/species/E_coli_K12/E_coli_K12_parameters.cfg +++ b/config/species/E_coli_K12/E_coli_K12_parameters.cfg @@ -9,7 +9,7 @@ #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.41 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.56 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 5 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 5 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.067 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile E_coli_K12_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile E_coli_K12_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/E_coli_K12/E_coli_K12_trans_shadow_bacterium.pbl b/config/species/E_coli_K12/E_coli_K12_trans_shadow_bacterium.pbl index 06e3d725..bb60ecc3 100644 --- a/config/species/E_coli_K12/E_coli_K12_trans_shadow_bacterium.pbl +++ b/config/species/E_coli_K12/E_coli_K12_trans_shadow_bacterium.pbl @@ -21,7 +21,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 3 diff --git a/config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg b/config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg index b12087a3..ca994edf 100644 --- a/config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg +++ b/config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 2 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 2 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.15 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.227 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile Xipophorus_maculatus_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile Xipophorus_maculatus_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/adorsata/adorsata_parameters.cfg b/config/species/adorsata/adorsata_parameters.cfg index be6c48ce..cb442970 100644 --- a/config/species/adorsata/adorsata_parameters.cfg +++ b/config/species/adorsata/adorsata_parameters.cfg @@ -18,7 +18,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -79,7 +79,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile generic_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile generic_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/aedes/aedes_parameters.cfg b/config/species/aedes/aedes_parameters.cfg index 54853067..199b0849 100644 --- a/config/species/aedes/aedes_parameters.cfg +++ b/config/species/aedes/aedes_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary stopCodonExcludedFromCDS false # make this 'true' if the CDS in the training set do not include the stop codon diff --git a/config/species/amphimedon/amphimedon_parameters.cfg b/config/species/amphimedon/amphimedon_parameters.cfg index 0c855bdc..369b28a8 100644 --- a/config/species/amphimedon/amphimedon_parameters.cfg +++ b/config/species/amphimedon/amphimedon_parameters.cfg @@ -8,7 +8,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -69,7 +69,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile amphimedon_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile amphimedon_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg b/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg index ca18e6b9..f38118a2 100644 --- a/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg +++ b/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.267 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile ancylostoma_ceylanicum_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile ancylostoma_ceylanicum_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/anidulans/anidulans_parameters.cfg b/config/species/anidulans/anidulans_parameters.cfg index 43193123..364c8b58 100644 --- a/config/species/anidulans/anidulans_parameters.cfg +++ b/config/species/anidulans/anidulans_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS in the training set do not include the stop codon diff --git a/config/species/anidulans/anidulans_weightmatrix.txt b/config/species/anidulans/anidulans_weightmatrix.txt index f9640523..8c9c3abb 100644 --- a/config/species/anidulans/anidulans_weightmatrix.txt +++ b/config/species/anidulans/anidulans_weightmatrix.txt @@ -1,7 +1,7 @@ # # This file contains a matrix used for weighing the training sequences # when given an input sequence. Let z = (da, dc, dg, dt) be the vector -# containing the differences in the relative nukleotide frequencies of +# containing the differences in the relative nucleotide frequencies of # two sequences, the input sequence and a training sequence. # Then the training sequence has weight proportional to # diff --git a/config/species/arabidopsis/arabidopsis_parameters.cfg b/config/species/arabidopsis/arabidopsis_parameters.cfg index 1575c1b7..e9605c72 100644 --- a/config/species/arabidopsis/arabidopsis_parameters.cfg +++ b/config/species/arabidopsis/arabidopsis_parameters.cfg @@ -1,13 +1,13 @@ # # parameters for Arabidopsis thaliana -# (revised paramters trained on whole genome annotation including UTR) +# (revised parameters trained on whole genome annotation including UTR) # date : 26.05.2007 # # # Properties for augustus #------------------------------------ -/augustus/verbosity 1 # 0-3, 0: only print the neccessary +/augustus/verbosity 1 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) diff --git a/config/species/arabidopsis/arabidopsis_weightmatrix.txt b/config/species/arabidopsis/arabidopsis_weightmatrix.txt index 75c7a21d..30f7cac7 100644 --- a/config/species/arabidopsis/arabidopsis_weightmatrix.txt +++ b/config/species/arabidopsis/arabidopsis_weightmatrix.txt @@ -1,7 +1,7 @@ # # This file contains a matrix used for weighing the training sequences # when given an input sequence. Let z = (da, dc, dg, dt) be the vector -# containing the differences in the relative nukleotide frequencies of +# containing the differences in the relative nucleotide frequencies of # two sequences, the input sequence and a training sequence. # Then the training sequence has weight proportional to # diff --git a/config/species/aspergillus_fumigatus/aspergillus_fumigatus_parameters.cfg b/config/species/aspergillus_fumigatus/aspergillus_fumigatus_parameters.cfg index d2ec370e..f624f41f 100644 --- a/config/species/aspergillus_fumigatus/aspergillus_fumigatus_parameters.cfg +++ b/config/species/aspergillus_fumigatus/aspergillus_fumigatus_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile aspergillus_fumigatus_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile aspergillus_fumigatus_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/aspergillus_nidulans/aspergillus_nidulans_parameters.cfg b/config/species/aspergillus_nidulans/aspergillus_nidulans_parameters.cfg index 35fd0fed..53470706 100644 --- a/config/species/aspergillus_nidulans/aspergillus_nidulans_parameters.cfg +++ b/config/species/aspergillus_nidulans/aspergillus_nidulans_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile aspergillus_nidulans_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile aspergillus_nidulans_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/aspergillus_oryzae/aspergillus_oryzae_parameters.cfg b/config/species/aspergillus_oryzae/aspergillus_oryzae_parameters.cfg index 91213881..0289eaa3 100644 --- a/config/species/aspergillus_oryzae/aspergillus_oryzae_parameters.cfg +++ b/config/species/aspergillus_oryzae/aspergillus_oryzae_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile aspergillus_oryzae_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile aspergillus_oryzae_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/aspergillus_terreus/aspergillus_terreus_parameters.cfg b/config/species/aspergillus_terreus/aspergillus_terreus_parameters.cfg index f0bb1789..e2809fc4 100644 --- a/config/species/aspergillus_terreus/aspergillus_terreus_parameters.cfg +++ b/config/species/aspergillus_terreus/aspergillus_terreus_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile aspergillus_terreus_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile aspergillus_terreus_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg b/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg index b8d3692e..f68a6c3e 100644 --- a/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg +++ b/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg @@ -9,7 +9,7 @@ #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.25 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.75 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 2 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 2 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.067 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile b_pseudomallei_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile b_pseudomallei_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1 b/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1 index 09c66d7e..ad8cf4f4 100644 --- a/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1 +++ b/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1 @@ -9,7 +9,7 @@ #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.25 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.75 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 2 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 2 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.067 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile b_pseudomallei_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile b_pseudomallei_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2 b/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2 index 09c66d7e..ad8cf4f4 100644 --- a/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2 +++ b/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2 @@ -9,7 +9,7 @@ #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.25 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.75 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 2 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 2 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.067 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile b_pseudomallei_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile b_pseudomallei_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/b_pseudomallei/b_pseudomallei_trans_shadow_bacterium.pbl b/config/species/b_pseudomallei/b_pseudomallei_trans_shadow_bacterium.pbl index 4167c3e4..9391a750 100644 --- a/config/species/b_pseudomallei/b_pseudomallei_trans_shadow_bacterium.pbl +++ b/config/species/b_pseudomallei/b_pseudomallei_trans_shadow_bacterium.pbl @@ -21,7 +21,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 3 diff --git a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg index 35102354..13048ce4 100644 --- a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg +++ b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.25 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.41 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 4 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 4 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.2 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.14 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile bombus_impatiens1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile bombus_impatiens1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1 b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1 index dcc668fb..57ba868a 100644 --- a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1 +++ b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.166 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile bombus_impatiens1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile bombus_impatiens1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2 b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2 index 0346f773..3500620a 100644 --- a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2 +++ b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.129 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile bombus_impatiens1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile bombus_impatiens1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3 b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3 index 8191d604..154cb452 100644 --- a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3 +++ b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.2125 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.556 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile bombus_impatiens1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile bombus_impatiens1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4 b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4 index 1d2b9513..8890fa70 100644 --- a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4 +++ b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.2 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.134 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile bombus_impatiens1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile bombus_impatiens1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5 b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5 index f6539131..d91a3a9a 100644 --- a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5 +++ b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.25 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.41 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 5 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 5 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.2 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.14 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile bombus_impatiens1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile bombus_impatiens1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg index a9025dd4..ee27a769 100644 --- a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg +++ b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg @@ -6,7 +6,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -55,7 +55,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.15 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.55 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 7 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 7 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.15 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.158 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile bombus_terrestris2_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile bombus_terrestris2_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1 b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1 index 6d7e01d9..35c40650 100644 --- a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1 +++ b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.149 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile honeybee1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile honeybee1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2 b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2 index 9032cce8..ac5a82b9 100644 --- a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2 +++ b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2 @@ -6,7 +6,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -55,7 +55,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.15 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.55 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 7 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 7 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.15 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.158 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile bombus_terrestris1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile bombus_terrestris1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3 b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3 index 88485673..34776fd6 100644 --- a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3 +++ b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3 @@ -6,7 +6,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -55,7 +55,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.15 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.55 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 7 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 7 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.15 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.158 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile bombus_terrestris1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile bombus_terrestris1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4 b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4 index 88485673..34776fd6 100644 --- a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4 +++ b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4 @@ -6,7 +6,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -55,7 +55,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.15 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.55 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 7 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 7 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.15 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.158 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile bombus_terrestris1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile bombus_terrestris1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/botrytis_cinerea/botrytis_cinerea_parameters.cfg b/config/species/botrytis_cinerea/botrytis_cinerea_parameters.cfg index 6a3100bc..9ad7629f 100644 --- a/config/species/botrytis_cinerea/botrytis_cinerea_parameters.cfg +++ b/config/species/botrytis_cinerea/botrytis_cinerea_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile botrytis_cinerea_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile botrytis_cinerea_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/brugia/brugia_parameters.cfg b/config/species/brugia/brugia_parameters.cfg index 1eb70caf..2a3917ec 100644 --- a/config/species/brugia/brugia_parameters.cfg +++ b/config/species/brugia/brugia_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 1 # 0-3, 0: only print the neccessary +/augustus/verbosity 1 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS in the training set do not include the stop codon diff --git a/config/species/brugia/brugia_weightmatrix.txt b/config/species/brugia/brugia_weightmatrix.txt index 46b2d13d..e3051930 100644 --- a/config/species/brugia/brugia_weightmatrix.txt +++ b/config/species/brugia/brugia_weightmatrix.txt @@ -1,7 +1,7 @@ # # This file contains a matrix used for weighing the training sequences # when given an input sequence. Let z = (da, dc, dg, dt) be the vector -# containing the differences in the relative nukleotide frequencies of +# containing the differences in the relative nucleotide frequencies of # two sequences, the input sequence and a training sequence. # Then the training sequence has weight proportional to # diff --git a/config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg b/config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg index ce715904..54e94eeb 100644 --- a/config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg +++ b/config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.195 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile c_elegans_trsk_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile c_elegans_trsk_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/cacao/cacao_parameters.cfg b/config/species/cacao/cacao_parameters.cfg index 5550d5a7..1f9d8999 100644 --- a/config/species/cacao/cacao_parameters.cfg +++ b/config/species/cacao/cacao_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.24 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -69,7 +69,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile cacao_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile cacao_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/caenorhabditis/caenorhabditis_parameters.cfg b/config/species/caenorhabditis/caenorhabditis_parameters.cfg index b5933127..d4588774 100644 --- a/config/species/caenorhabditis/caenorhabditis_parameters.cfg +++ b/config/species/caenorhabditis/caenorhabditis_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -57,7 +57,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 /Constant/amberprob 0.18 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -69,7 +69,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile caenorhabditis_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile caenorhabditis_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/caenorhabditis/caenorhabditis_trans_shadow_partial_utr.pbl b/config/species/caenorhabditis/caenorhabditis_trans_shadow_partial_utr.pbl index ce0bacff..e1176c75 100644 --- a/config/species/caenorhabditis/caenorhabditis_trans_shadow_partial_utr.pbl +++ b/config/species/caenorhabditis/caenorhabditis_trans_shadow_partial_utr.pbl @@ -90,7 +90,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 71 diff --git a/config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg b/config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg index da4235e8..0c44759b 100644 --- a/config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg +++ b/config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile camponotus_floridanus_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile camponotus_floridanus_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/candida_albicans/candida_albicans_parameters.cfg b/config/species/candida_albicans/candida_albicans_parameters.cfg index b80c5a34..d8c82158 100644 --- a/config/species/candida_albicans/candida_albicans_parameters.cfg +++ b/config/species/candida_albicans/candida_albicans_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile candida_albicans_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile candida_albicans_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/candida_guilliermondii/candida_guilliermondii_parameters.cfg b/config/species/candida_guilliermondii/candida_guilliermondii_parameters.cfg index 71c2e3b7..74396423 100644 --- a/config/species/candida_guilliermondii/candida_guilliermondii_parameters.cfg +++ b/config/species/candida_guilliermondii/candida_guilliermondii_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile candida_guilliermondii_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile candida_guilliermondii_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/candida_tropicalis/candida_tropicalis_parameters.cfg b/config/species/candida_tropicalis/candida_tropicalis_parameters.cfg index 1de2d792..1132d6eb 100644 --- a/config/species/candida_tropicalis/candida_tropicalis_parameters.cfg +++ b/config/species/candida_tropicalis/candida_tropicalis_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile candida_tropicalis_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile candida_tropicalis_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/chaetomium_globosum/chaetomium_globosum_parameters.cfg b/config/species/chaetomium_globosum/chaetomium_globosum_parameters.cfg index 335fe60a..f4447a8f 100644 --- a/config/species/chaetomium_globosum/chaetomium_globosum_parameters.cfg +++ b/config/species/chaetomium_globosum/chaetomium_globosum_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile chaetomium_globosum_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile chaetomium_globosum_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/chicken/chicken_parameters.cfg b/config/species/chicken/chicken_parameters.cfg index 2a955db3..d2406a8a 100644 --- a/config/species/chicken/chicken_parameters.cfg +++ b/config/species/chicken/chicken_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 1000000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.37 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.61 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 10 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 10 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile chicken_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile chicken_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/chiloscyllium/chiloscyllium_parameters.cfg b/config/species/chiloscyllium/chiloscyllium_parameters.cfg index 888859e8..9de9ce49 100644 --- a/config/species/chiloscyllium/chiloscyllium_parameters.cfg +++ b/config/species/chiloscyllium/chiloscyllium_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.15 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile chiloscyllium_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile chiloscyllium_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1 b/config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1 index 0f5a4129..b5ae0522 100644 --- a/config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1 +++ b/config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile chiloscyllium_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile chiloscyllium_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/chlamy2011/chlamy2011_parameters.cfg b/config/species/chlamy2011/chlamy2011_parameters.cfg index 18cddefe..70d6b66f 100644 --- a/config/species/chlamy2011/chlamy2011_parameters.cfg +++ b/config/species/chlamy2011/chlamy2011_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -68,7 +68,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile chlamy2011_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile chlamy2011_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/chlamy2011/chlamy2011_trans_shadow_partial.pbl b/config/species/chlamy2011/chlamy2011_trans_shadow_partial.pbl index 3f7cf227..2dab9f38 100644 --- a/config/species/chlamy2011/chlamy2011_trans_shadow_partial.pbl +++ b/config/species/chlamy2011/chlamy2011_trans_shadow_partial.pbl @@ -67,7 +67,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 47 diff --git a/config/species/chlamy2011/chlamy2011_trans_shadow_partial_utr.pbl b/config/species/chlamy2011/chlamy2011_trans_shadow_partial_utr.pbl index 23ab2f9e..d2d93484 100644 --- a/config/species/chlamy2011/chlamy2011_trans_shadow_partial_utr.pbl +++ b/config/species/chlamy2011/chlamy2011_trans_shadow_partial_utr.pbl @@ -90,7 +90,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 71 diff --git a/config/species/chlamydomonas/chlamydomonas_parameters.cfg b/config/species/chlamydomonas/chlamydomonas_parameters.cfg index ddb06cab..5f96cf9f 100644 --- a/config/species/chlamydomonas/chlamydomonas_parameters.cfg +++ b/config/species/chlamydomonas/chlamydomonas_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile chlamydomonas_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile chlamydomonas_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial.pbl b/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial.pbl index 3f7cf227..2dab9f38 100644 --- a/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial.pbl +++ b/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial.pbl @@ -67,7 +67,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 47 diff --git a/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial_utr.pbl b/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial_utr.pbl index 8fdf3dc5..01b63f7d 100644 --- a/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial_utr.pbl +++ b/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial_utr.pbl @@ -90,7 +90,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 71 diff --git a/config/species/chlorella/chlorella_parameters.cfg b/config/species/chlorella/chlorella_parameters.cfg index 7b3b5b22..728a46fa 100644 --- a/config/species/chlorella/chlorella_parameters.cfg +++ b/config/species/chlorella/chlorella_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile chlorella_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile chlorella_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/ciona/ciona_parameters.cfg b/config/species/ciona/ciona_parameters.cfg index 49402d0c..95bea3f0 100644 --- a/config/species/ciona/ciona_parameters.cfg +++ b/config/species/ciona/ciona_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.15 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile ciona_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile ciona_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/ciona/ciona_parameters.cfg.orig1 b/config/species/ciona/ciona_parameters.cfg.orig1 index 978f46d8..9a0ed15e 100644 --- a/config/species/ciona/ciona_parameters.cfg.orig1 +++ b/config/species/ciona/ciona_parameters.cfg.orig1 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile ciona_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile ciona_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/coccidioides_immitis/coccidioides_immitis_parameters.cfg b/config/species/coccidioides_immitis/coccidioides_immitis_parameters.cfg index b4a01d93..1638c551 100644 --- a/config/species/coccidioides_immitis/coccidioides_immitis_parameters.cfg +++ b/config/species/coccidioides_immitis/coccidioides_immitis_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile coccidioides_immitis_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile coccidioides_immitis_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/coprinus/coprinus_parameters.cfg b/config/species/coprinus/coprinus_parameters.cfg index 20cedbfb..953921a2 100644 --- a/config/species/coprinus/coprinus_parameters.cfg +++ b/config/species/coprinus/coprinus_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS in the training set do not include the stop codon diff --git a/config/species/coprinus/coprinus_weightmatrix.txt b/config/species/coprinus/coprinus_weightmatrix.txt index f9640523..8c9c3abb 100644 --- a/config/species/coprinus/coprinus_weightmatrix.txt +++ b/config/species/coprinus/coprinus_weightmatrix.txt @@ -1,7 +1,7 @@ # # This file contains a matrix used for weighing the training sequences # when given an input sequence. Let z = (da, dc, dg, dt) be the vector -# containing the differences in the relative nukleotide frequencies of +# containing the differences in the relative nucleotide frequencies of # two sequences, the input sequence and a training sequence. # Then the training sequence has weight proportional to # diff --git a/config/species/coprinus_cinereus/coprinus_cinereus_parameters.cfg b/config/species/coprinus_cinereus/coprinus_cinereus_parameters.cfg index 31831d10..f0fb8ef7 100644 --- a/config/species/coprinus_cinereus/coprinus_cinereus_parameters.cfg +++ b/config/species/coprinus_cinereus/coprinus_cinereus_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile coprinus_cinereus_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile coprinus_cinereus_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/coyote_tobacco/coyote_tobacco_parameters.cfg b/config/species/coyote_tobacco/coyote_tobacco_parameters.cfg index ce6c3a39..9378dc72 100644 --- a/config/species/coyote_tobacco/coyote_tobacco_parameters.cfg +++ b/config/species/coyote_tobacco/coyote_tobacco_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.225 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile coyote_tobacco_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile coyote_tobacco_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/coyote_tobacco/coyote_tobacco_trans_shadow_partial_utr.pbl b/config/species/coyote_tobacco/coyote_tobacco_trans_shadow_partial_utr.pbl index 0464ee18..54b76161 100644 --- a/config/species/coyote_tobacco/coyote_tobacco_trans_shadow_partial_utr.pbl +++ b/config/species/coyote_tobacco/coyote_tobacco_trans_shadow_partial_utr.pbl @@ -90,7 +90,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 71 diff --git a/config/species/cryptococcus/cryptococcus_parameters.cfg b/config/species/cryptococcus/cryptococcus_parameters.cfg index 990df9b7..8ea82fa6 100644 --- a/config/species/cryptococcus/cryptococcus_parameters.cfg +++ b/config/species/cryptococcus/cryptococcus_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS in the training set do not include the stop codon diff --git a/config/species/cryptococcus/cryptococcus_weightmatrix.txt b/config/species/cryptococcus/cryptococcus_weightmatrix.txt index f9640523..8c9c3abb 100644 --- a/config/species/cryptococcus/cryptococcus_weightmatrix.txt +++ b/config/species/cryptococcus/cryptococcus_weightmatrix.txt @@ -1,7 +1,7 @@ # # This file contains a matrix used for weighing the training sequences # when given an input sequence. Let z = (da, dc, dg, dt) be the vector -# containing the differences in the relative nukleotide frequencies of +# containing the differences in the relative nucleotide frequencies of # two sequences, the input sequence and a training sequence. # Then the training sequence has weight proportional to # diff --git a/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_parameters.cfg b/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_parameters.cfg index dc358cdc..c8f431e9 100644 --- a/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_parameters.cfg +++ b/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile cryptococcus_neoformans_gattii_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile cryptococcus_neoformans_gattii_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_parameters.cfg b/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_parameters.cfg index 9fd426a9..e4c6008a 100644 --- a/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_parameters.cfg +++ b/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile cryptococcus_neoformans_neoformans_B_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile cryptococcus_neoformans_neoformans_B_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_parameters.cfg b/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_parameters.cfg index 34792bae..a0491c42 100644 --- a/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_parameters.cfg +++ b/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile cryptococcus_neoformans_neoformans_JEC21_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile cryptococcus_neoformans_neoformans_JEC21_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/culex/culex_parameters.cfg b/config/species/culex/culex_parameters.cfg index 2ea5af2b..6a5068cf 100644 --- a/config/species/culex/culex_parameters.cfg +++ b/config/species/culex/culex_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile culex_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile culex_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/culex/culex_parameters.old.cfg b/config/species/culex/culex_parameters.old.cfg index 3e9447b8..2a6fb1b8 100644 --- a/config/species/culex/culex_parameters.old.cfg +++ b/config/species/culex/culex_parameters.old.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile culex_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile culex_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/culex/culex_trans_shadow_partial_utr.pbl b/config/species/culex/culex_trans_shadow_partial_utr.pbl index 9e1eac7e..c409b8c0 100644 --- a/config/species/culex/culex_trans_shadow_partial_utr.pbl +++ b/config/species/culex/culex_trans_shadow_partial_utr.pbl @@ -68,7 +68,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 49 diff --git a/config/species/debaryomyces_hansenii/debaryomyces_hansenii_parameters.cfg b/config/species/debaryomyces_hansenii/debaryomyces_hansenii_parameters.cfg index 8d1b7600..9c5e4748 100644 --- a/config/species/debaryomyces_hansenii/debaryomyces_hansenii_parameters.cfg +++ b/config/species/debaryomyces_hansenii/debaryomyces_hansenii_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile debaryomyces_hansenii_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile debaryomyces_hansenii_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/elephant_shark/elephant_shark_parameters.cfg b/config/species/elephant_shark/elephant_shark_parameters.cfg index 1f16e22a..5702da66 100644 --- a/config/species/elephant_shark/elephant_shark_parameters.cfg +++ b/config/species/elephant_shark/elephant_shark_parameters.cfg @@ -11,7 +11,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -59,7 +59,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 5 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 5 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -71,7 +71,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile elephant_shark_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile elephant_shark_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_parameters.cfg b/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_parameters.cfg index 22c37dfe..381743cd 100644 --- a/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_parameters.cfg +++ b/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile encephalitozoon_cuniculi_GB_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile encephalitozoon_cuniculi_GB_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/eremothecium_gossypii/eremothecium_gossypii_parameters.cfg b/config/species/eremothecium_gossypii/eremothecium_gossypii_parameters.cfg index e3156f61..67d19b12 100644 --- a/config/species/eremothecium_gossypii/eremothecium_gossypii_parameters.cfg +++ b/config/species/eremothecium_gossypii/eremothecium_gossypii_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile eremothecium_gossypii_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile eremothecium_gossypii_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/fly/fly_parameters.cfg b/config/species/fly/fly_parameters.cfg index e38b91f1..bdb7effc 100644 --- a/config/species/fly/fly_parameters.cfg +++ b/config/species/fly/fly_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -55,7 +55,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.50 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.34 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -67,7 +67,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile fly_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile fly_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/fly_exp/fly_exp_parameters.cfg b/config/species/fly_exp/fly_exp_parameters.cfg index 37fbba55..739093b5 100644 --- a/config/species/fly_exp/fly_exp_parameters.cfg +++ b/config/species/fly_exp/fly_exp_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -55,7 +55,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.50 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.34 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile fly_exp_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile fly_exp_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/fusarium/fusarium_parameters.cfg b/config/species/fusarium/fusarium_parameters.cfg index 7c38bab4..cf50216a 100644 --- a/config/species/fusarium/fusarium_parameters.cfg +++ b/config/species/fusarium/fusarium_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS in the training set do not include the stop codon diff --git a/config/species/fusarium/fusarium_weightmatrix.txt b/config/species/fusarium/fusarium_weightmatrix.txt index f9640523..8c9c3abb 100644 --- a/config/species/fusarium/fusarium_weightmatrix.txt +++ b/config/species/fusarium/fusarium_weightmatrix.txt @@ -1,7 +1,7 @@ # # This file contains a matrix used for weighing the training sequences # when given an input sequence. Let z = (da, dc, dg, dt) be the vector -# containing the differences in the relative nukleotide frequencies of +# containing the differences in the relative nucleotide frequencies of # two sequences, the input sequence and a training sequence. # Then the training sequence has weight proportional to # diff --git a/config/species/fusarium_graminearum/fusarium_graminearum_parameters.cfg b/config/species/fusarium_graminearum/fusarium_graminearum_parameters.cfg index 3ddfde8c..68db4fd1 100644 --- a/config/species/fusarium_graminearum/fusarium_graminearum_parameters.cfg +++ b/config/species/fusarium_graminearum/fusarium_graminearum_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile fusarium_graminearum_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile fusarium_graminearum_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/galdieria/galdieria_parameters.cfg b/config/species/galdieria/galdieria_parameters.cfg index 27bc454b..dca452c6 100644 --- a/config/species/galdieria/galdieria_parameters.cfg +++ b/config/species/galdieria/galdieria_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary stopCodonExcludedFromCDS false # make this 'true' if the CDS in the training set do not include the stop codon diff --git a/config/species/galdieria/galdieria_trans_shadow_partial_utr.pbl b/config/species/galdieria/galdieria_trans_shadow_partial_utr.pbl index 82d62d83..65621d6a 100644 --- a/config/species/galdieria/galdieria_trans_shadow_partial_utr.pbl +++ b/config/species/galdieria/galdieria_trans_shadow_partial_utr.pbl @@ -91,7 +91,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 71 diff --git a/config/species/galdieria/galdieria_weightmatrix.txt b/config/species/galdieria/galdieria_weightmatrix.txt index 46b2d13d..e3051930 100644 --- a/config/species/galdieria/galdieria_weightmatrix.txt +++ b/config/species/galdieria/galdieria_weightmatrix.txt @@ -1,7 +1,7 @@ # # This file contains a matrix used for weighing the training sequences # when given an input sequence. Let z = (da, dc, dg, dt) be the vector -# containing the differences in the relative nukleotide frequencies of +# containing the differences in the relative nucleotide frequencies of # two sequences, the input sequence and a training sequence. # Then the training sequence has weight proportional to # diff --git a/config/species/generic/generic_parameters.cfg b/config/species/generic/generic_parameters.cfg index 6245a4a0..4234d250 100644 --- a/config/species/generic/generic_parameters.cfg +++ b/config/species/generic/generic_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile generic_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile generic_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg b/config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg index ec04cc07..358d4011 100644 --- a/config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg +++ b/config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.15 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile heliconius_melpomene1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile heliconius_melpomene1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/histoplasma/histoplasma_parameters.cfg b/config/species/histoplasma/histoplasma_parameters.cfg index 4bb4b402..2472de1b 100644 --- a/config/species/histoplasma/histoplasma_parameters.cfg +++ b/config/species/histoplasma/histoplasma_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS in the training set do not include the stop codon diff --git a/config/species/histoplasma/histoplasma_weightmatrix.txt b/config/species/histoplasma/histoplasma_weightmatrix.txt index f9640523..8c9c3abb 100644 --- a/config/species/histoplasma/histoplasma_weightmatrix.txt +++ b/config/species/histoplasma/histoplasma_weightmatrix.txt @@ -1,7 +1,7 @@ # # This file contains a matrix used for weighing the training sequences # when given an input sequence. Let z = (da, dc, dg, dt) be the vector -# containing the differences in the relative nukleotide frequencies of +# containing the differences in the relative nucleotide frequencies of # two sequences, the input sequence and a training sequence. # Then the training sequence has weight proportional to # diff --git a/config/species/histoplasma_capsulatum/histoplasma_capsulatum_parameters.cfg b/config/species/histoplasma_capsulatum/histoplasma_capsulatum_parameters.cfg index 79f390ec..a7e0f285 100644 --- a/config/species/histoplasma_capsulatum/histoplasma_capsulatum_parameters.cfg +++ b/config/species/histoplasma_capsulatum/histoplasma_capsulatum_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile histoplasma_capsulatum_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile histoplasma_capsulatum_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/honeybee1/honeybee1_parameters.cfg b/config/species/honeybee1/honeybee1_parameters.cfg index c871e088..5e1d8852 100644 --- a/config/species/honeybee1/honeybee1_parameters.cfg +++ b/config/species/honeybee1/honeybee1_parameters.cfg @@ -6,7 +6,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -55,7 +55,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.15 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.55 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 7 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 7 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.15 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.133 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile honeybee1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile honeybee1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/honeybee1/honeybee1_parameters.cfg.orig1 b/config/species/honeybee1/honeybee1_parameters.cfg.orig1 index 6d7e01d9..35c40650 100644 --- a/config/species/honeybee1/honeybee1_parameters.cfg.orig1 +++ b/config/species/honeybee1/honeybee1_parameters.cfg.orig1 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.149 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile honeybee1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile honeybee1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/human/human_parameters.cfg b/config/species/human/human_parameters.cfg index b452cd0c..235cae69 100644 --- a/config/species/human/human_parameters.cfg +++ b/config/species/human/human_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 2000000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does do not include the stop codon (both for input and output) diff --git a/config/species/human/human_trans_shadow_partial_utr.pbl b/config/species/human/human_trans_shadow_partial_utr.pbl index 0464ee18..54b76161 100644 --- a/config/species/human/human_trans_shadow_partial_utr.pbl +++ b/config/species/human/human_trans_shadow_partial_utr.pbl @@ -90,7 +90,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 71 diff --git a/config/species/human/human_weightmatrix.txt b/config/species/human/human_weightmatrix.txt index 833bdd41..a6ea659c 100644 --- a/config/species/human/human_weightmatrix.txt +++ b/config/species/human/human_weightmatrix.txt @@ -1,7 +1,7 @@ # # This file contains a matrix used for weighing the training sequences # when given an input sequence. Let z = (da, dc, dg, dt) be the vector -# containing the differences in the relative nukleotide frequencies of +# containing the differences in the relative nucleotide frequencies of # two sequences, the input sequence and a training sequence. # Then the training sequence has weight proportional to # diff --git a/config/species/japaneselamprey/japaneselamprey_parameters.cfg b/config/species/japaneselamprey/japaneselamprey_parameters.cfg index 30e1fad2..162e6e77 100644 --- a/config/species/japaneselamprey/japaneselamprey_parameters.cfg +++ b/config/species/japaneselamprey/japaneselamprey_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 4 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 4 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.198 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile japaneselamprey_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile japaneselamprey_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/kluyveromyces_lactis/kluyveromyces_lactis_parameters.cfg b/config/species/kluyveromyces_lactis/kluyveromyces_lactis_parameters.cfg index 61aae1cb..c23537e5 100644 --- a/config/species/kluyveromyces_lactis/kluyveromyces_lactis_parameters.cfg +++ b/config/species/kluyveromyces_lactis/kluyveromyces_lactis_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile kluyveromyces_lactis_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile kluyveromyces_lactis_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/laccaria_bicolor/laccaria_bicolor_parameters.cfg b/config/species/laccaria_bicolor/laccaria_bicolor_parameters.cfg index 4337b4ed..f4565167 100644 --- a/config/species/laccaria_bicolor/laccaria_bicolor_parameters.cfg +++ b/config/species/laccaria_bicolor/laccaria_bicolor_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile laccaria_bicolor_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile laccaria_bicolor_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg b/config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg index 11c4ce62..28d4ecc3 100644 --- a/config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg +++ b/config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg @@ -8,7 +8,7 @@ # Properties for augustus #------------------------------------ genemodel intronless # do not consider introns, only single-exon genes -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 /Constant/amberprob 0.372 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile leishmania_tarentolae_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile leishmania_tarentolae_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_parameters.cfg b/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_parameters.cfg index 84872ae3..c21331fc 100644 --- a/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_parameters.cfg +++ b/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile lodderomyces_elongisporus_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile lodderomyces_elongisporus_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/magnaporthe_grisea/magnaporthe_grisea_parameters.cfg b/config/species/magnaporthe_grisea/magnaporthe_grisea_parameters.cfg index ce5ab00f..863887a0 100644 --- a/config/species/magnaporthe_grisea/magnaporthe_grisea_parameters.cfg +++ b/config/species/magnaporthe_grisea/magnaporthe_grisea_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile magnaporthe_grisea_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile magnaporthe_grisea_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/maize/maize_parameters.cfg b/config/species/maize/maize_parameters.cfg index 644b610c..02516c28 100644 --- a/config/species/maize/maize_parameters.cfg +++ b/config/species/maize/maize_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -53,7 +53,7 @@ keep_viterbi true # set to true if all Viterbi transcripts should be r /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.35 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.60 # minimal and maximal percentage of c or g -/Constant/decomp_num_steps 10 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 10 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.228 /Constant/amberprob 0.284 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -63,7 +63,7 @@ keep_viterbi true # set to true if all Viterbi transcripts should be r # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile maize_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile maize_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/maize5/maize5_parameters.cfg b/config/species/maize5/maize5_parameters.cfg index 03f319ca..a58a1e81 100644 --- a/config/species/maize5/maize5_parameters.cfg +++ b/config/species/maize5/maize5_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 3 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 3 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.304 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile maize5_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile maize5_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg b/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg index 8c1dde33..9edd7098 100644 --- a/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg +++ b/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile mnemiopsis_leidyi_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile mnemiopsis_leidyi_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/nasonia/nasonia_parameters.cfg b/config/species/nasonia/nasonia_parameters.cfg index 52c546ca..f988a975 100644 --- a/config/species/nasonia/nasonia_parameters.cfg +++ b/config/species/nasonia/nasonia_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile nasonia_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile nasonia_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg b/config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg index f9f10a4b..7ab81385 100644 --- a/config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg +++ b/config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile nematostella_vectensis_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile nematostella_vectensis_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/neurospora/neurospora_parameters.cfg b/config/species/neurospora/neurospora_parameters.cfg index 26996765..dd0341d6 100644 --- a/config/species/neurospora/neurospora_parameters.cfg +++ b/config/species/neurospora/neurospora_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS in the training set do not include the stop codon diff --git a/config/species/neurospora/neurospora_weightmatrix.txt b/config/species/neurospora/neurospora_weightmatrix.txt index f9640523..8c9c3abb 100644 --- a/config/species/neurospora/neurospora_weightmatrix.txt +++ b/config/species/neurospora/neurospora_weightmatrix.txt @@ -1,7 +1,7 @@ # # This file contains a matrix used for weighing the training sequences # when given an input sequence. Let z = (da, dc, dg, dt) be the vector -# containing the differences in the relative nukleotide frequencies of +# containing the differences in the relative nucleotide frequencies of # two sequences, the input sequence and a training sequence. # Then the training sequence has weight proportional to # diff --git a/config/species/neurospora_crassa/neurospora_crassa_parameters.cfg b/config/species/neurospora_crassa/neurospora_crassa_parameters.cfg index 7aec999a..c827bbe5 100644 --- a/config/species/neurospora_crassa/neurospora_crassa_parameters.cfg +++ b/config/species/neurospora_crassa/neurospora_crassa_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile neurospora_crassa_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile neurospora_crassa_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/parasteatoda/parasteatoda_parameters.cfg b/config/species/parasteatoda/parasteatoda_parameters.cfg index 98c4fb08..08f2280e 100644 --- a/config/species/parasteatoda/parasteatoda_parameters.cfg +++ b/config/species/parasteatoda/parasteatoda_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.162 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile parasteatoda_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile parasteatoda_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/pchrysosporium/pchrysosporium_parameters.cfg b/config/species/pchrysosporium/pchrysosporium_parameters.cfg index 9b829dca..32ec1e3e 100644 --- a/config/species/pchrysosporium/pchrysosporium_parameters.cfg +++ b/config/species/pchrysosporium/pchrysosporium_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS in the training set do not include the stop codon diff --git a/config/species/pchrysosporium/pchrysosporium_weightmatrix.txt b/config/species/pchrysosporium/pchrysosporium_weightmatrix.txt index f9640523..8c9c3abb 100644 --- a/config/species/pchrysosporium/pchrysosporium_weightmatrix.txt +++ b/config/species/pchrysosporium/pchrysosporium_weightmatrix.txt @@ -1,7 +1,7 @@ # # This file contains a matrix used for weighing the training sequences # when given an input sequence. Let z = (da, dc, dg, dt) be the vector -# containing the differences in the relative nukleotide frequencies of +# containing the differences in the relative nucleotide frequencies of # two sequences, the input sequence and a training sequence. # Then the training sequence has weight proportional to # diff --git a/config/species/pea_aphid/pea_aphid_parameters.cfg b/config/species/pea_aphid/pea_aphid_parameters.cfg index fefafb3d..2114b43b 100644 --- a/config/species/pea_aphid/pea_aphid_parameters.cfg +++ b/config/species/pea_aphid/pea_aphid_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -68,7 +68,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile pea_aphid_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile pea_aphid_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/pea_aphid/pea_aphid_trans_shadow_partial_utr.pbl b/config/species/pea_aphid/pea_aphid_trans_shadow_partial_utr.pbl index 74a70086..b25f8caf 100644 --- a/config/species/pea_aphid/pea_aphid_trans_shadow_partial_utr.pbl +++ b/config/species/pea_aphid/pea_aphid_trans_shadow_partial_utr.pbl @@ -90,7 +90,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 71 diff --git a/config/species/pfalciparum/pfalciparum_parameters.cfg b/config/species/pfalciparum/pfalciparum_parameters.cfg index 0e167150..6901dd6c 100644 --- a/config/species/pfalciparum/pfalciparum_parameters.cfg +++ b/config/species/pfalciparum/pfalciparum_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -50,7 +50,7 @@ keep_viterbi true # set to true if all Viterbi transcripts should be r /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob .13 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ keep_viterbi true # set to true if all Viterbi transcripts should be r # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile pfalciparum_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile pfalciparum_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/pfalciparum/pfalciparum_trans_shadow_partial.pbl b/config/species/pfalciparum/pfalciparum_trans_shadow_partial.pbl index 355dc4e2..1500eb05 100644 --- a/config/species/pfalciparum/pfalciparum_trans_shadow_partial.pbl +++ b/config/species/pfalciparum/pfalciparum_trans_shadow_partial.pbl @@ -67,7 +67,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 47 diff --git a/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_parameters.cfg b/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_parameters.cfg index b21f0c62..7899a22a 100644 --- a/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_parameters.cfg +++ b/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile phanerochaete_chrysosporium_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile phanerochaete_chrysosporium_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/pichia_stipitis/pichia_stipitis_parameters.cfg b/config/species/pichia_stipitis/pichia_stipitis_parameters.cfg index 3a156e9a..ef6b35d3 100644 --- a/config/species/pichia_stipitis/pichia_stipitis_parameters.cfg +++ b/config/species/pichia_stipitis/pichia_stipitis_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile pichia_stipitis_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile pichia_stipitis_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/pisaster/pisaster_parameters.cfg b/config/species/pisaster/pisaster_parameters.cfg index 9e56357d..19723a50 100644 --- a/config/species/pisaster/pisaster_parameters.cfg +++ b/config/species/pisaster/pisaster_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.243 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile pisaster_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile pisaster_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/pneumocystis/pneumocystis_parameters.cfg b/config/species/pneumocystis/pneumocystis_parameters.cfg index 8b4a447f..dd60f3ea 100644 --- a/config/species/pneumocystis/pneumocystis_parameters.cfg +++ b/config/species/pneumocystis/pneumocystis_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile pneumocystis_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile pneumocystis_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/rhincodon/rhincodon_parameters.cfg b/config/species/rhincodon/rhincodon_parameters.cfg index 3fe9e69f..ded819fa 100644 --- a/config/species/rhincodon/rhincodon_parameters.cfg +++ b/config/species/rhincodon/rhincodon_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.15 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile rhincodon_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile rhincodon_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/rhincodon/rhincodon_parameters.cfg.orig1 b/config/species/rhincodon/rhincodon_parameters.cfg.orig1 index 13166a64..ea20cd95 100644 --- a/config/species/rhincodon/rhincodon_parameters.cfg.orig1 +++ b/config/species/rhincodon/rhincodon_parameters.cfg.orig1 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile rhincodon2_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile rhincodon2_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/rhizopus_oryzae/rhizopus_oryzae_parameters.cfg b/config/species/rhizopus_oryzae/rhizopus_oryzae_parameters.cfg index 4b2e265d..96529108 100644 --- a/config/species/rhizopus_oryzae/rhizopus_oryzae_parameters.cfg +++ b/config/species/rhizopus_oryzae/rhizopus_oryzae_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile rhizopus_oryzae_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile rhizopus_oryzae_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/rhodnius/rhodnius_parameters.cfg b/config/species/rhodnius/rhodnius_parameters.cfg index aaa08d8a..c3db6d2b 100644 --- a/config/species/rhodnius/rhodnius_parameters.cfg +++ b/config/species/rhodnius/rhodnius_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.17 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile rhodnius_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile rhodnius_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/rice/rice_parameters.cfg b/config/species/rice/rice_parameters.cfg index 08869800..34842fad 100644 --- a/config/species/rice/rice_parameters.cfg +++ b/config/species/rice/rice_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.38 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.51 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 4 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 4 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.28 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile rice_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile rice_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/s_aureus/s_aureus_parameters.cfg b/config/species/s_aureus/s_aureus_parameters.cfg index 5defa6b5..c4b5aa3c 100644 --- a/config/species/s_aureus/s_aureus_parameters.cfg +++ b/config/species/s_aureus/s_aureus_parameters.cfg @@ -9,7 +9,7 @@ #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 2000000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.22 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.42 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 2 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 2 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.067 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile s_aureus_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile s_aureus_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/s_aureus/s_aureus_trans_shadow_bacterium.pbl b/config/species/s_aureus/s_aureus_trans_shadow_bacterium.pbl index 4167c3e4..9391a750 100644 --- a/config/species/s_aureus/s_aureus_trans_shadow_bacterium.pbl +++ b/config/species/s_aureus/s_aureus_trans_shadow_bacterium.pbl @@ -21,7 +21,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 3 diff --git a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg index ab4c39cd..56740853 100644 --- a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg +++ b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg @@ -9,7 +9,7 @@ #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 2000000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.25 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.75 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 5 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 5 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.067 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile s_pneumoniae_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile s_pneumoniae_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1 b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1 index 9ded31eb..2a10a690 100644 --- a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1 +++ b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1 @@ -9,7 +9,7 @@ #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 2000000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.25 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.75 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 2 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 2 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.067 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile s_pneumoniae_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile s_pneumoniae_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2 b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2 index 22052c9f..9fa954f2 100644 --- a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2 +++ b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2 @@ -9,7 +9,7 @@ #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 2000000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.25 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.75 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 3 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 3 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.067 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile s_pneumoniae_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile s_pneumoniae_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3 b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3 index 818d78b4..dd3fccb9 100644 --- a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3 +++ b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3 @@ -9,7 +9,7 @@ #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 2000000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.25 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.75 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 3 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 3 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.067 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile s_pneumoniae_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile s_pneumoniae_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4 b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4 index 239df8c3..a5abb85e 100644 --- a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4 +++ b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4 @@ -9,7 +9,7 @@ #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 2000000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.25 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.75 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 3 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 3 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.067 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile s_pneumoniae_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile s_pneumoniae_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/s_pneumoniae/s_pneumoniae_trans_shadow_bacterium.pbl b/config/species/s_pneumoniae/s_pneumoniae_trans_shadow_bacterium.pbl index 4167c3e4..9391a750 100644 --- a/config/species/s_pneumoniae/s_pneumoniae_trans_shadow_bacterium.pbl +++ b/config/species/s_pneumoniae/s_pneumoniae_trans_shadow_bacterium.pbl @@ -21,7 +21,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 3 diff --git a/config/species/saccharomyces/saccharomyces_parameters.cfg b/config/species/saccharomyces/saccharomyces_parameters.cfg index 26eaa20c..a325f02d 100644 --- a/config/species/saccharomyces/saccharomyces_parameters.cfg +++ b/config/species/saccharomyces/saccharomyces_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS in the training set do not include the stop codon diff --git a/config/species/saccharomyces/saccharomyces_weightmatrix.txt b/config/species/saccharomyces/saccharomyces_weightmatrix.txt index f9640523..8c9c3abb 100644 --- a/config/species/saccharomyces/saccharomyces_weightmatrix.txt +++ b/config/species/saccharomyces/saccharomyces_weightmatrix.txt @@ -1,7 +1,7 @@ # # This file contains a matrix used for weighing the training sequences # when given an input sequence. Let z = (da, dc, dg, dt) be the vector -# containing the differences in the relative nukleotide frequencies of +# containing the differences in the relative nucleotide frequencies of # two sequences, the input sequence and a training sequence. # Then the training sequence has weight proportional to # diff --git a/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_parameters.cfg b/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_parameters.cfg index 5fb0ad58..b22560ab 100644 --- a/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_parameters.cfg +++ b/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile saccharomyces_cerevisiae_S288C_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile saccharomyces_cerevisiae_S288C_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_parameters.cfg b/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_parameters.cfg index 45cdd3a8..8490706f 100644 --- a/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_parameters.cfg +++ b/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile saccharomyces_cerevisiae_rm11-1a_1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile saccharomyces_cerevisiae_rm11-1a_1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/schistosoma/schistosoma_parameters.cfg b/config/species/schistosoma/schistosoma_parameters.cfg index f0abdc9e..05729463 100644 --- a/config/species/schistosoma/schistosoma_parameters.cfg +++ b/config/species/schistosoma/schistosoma_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -63,7 +63,7 @@ keep_viterbi true # set to true if all Viterbi transcripts should be r # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile schistosoma_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile schistosoma_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/schistosoma/schistosoma_parameters.cfg.opt b/config/species/schistosoma/schistosoma_parameters.cfg.opt index ec392e04..99faa4ea 100644 --- a/config/species/schistosoma/schistosoma_parameters.cfg.opt +++ b/config/species/schistosoma/schistosoma_parameters.cfg.opt @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -63,7 +63,7 @@ maxtranscripts -1 # maximum number of reported transcripts per gene (-1: # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile generic_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile generic_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/schistosoma2/schistosoma2_parameters.cfg b/config/species/schistosoma2/schistosoma2_parameters.cfg index 28db8ce0..9ed02706 100644 --- a/config/species/schistosoma2/schistosoma2_parameters.cfg +++ b/config/species/schistosoma2/schistosoma2_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include the stop codon (training and prediction) min_intron_len 30 # 31 is also the sum of signal models in intron + 1 (minimum internal part len) @@ -56,7 +56,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.43 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 180 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.155 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile schistosoma2_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile schistosoma2_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_parameters.cfg b/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_parameters.cfg index fc4af533..c12c7f4a 100644 --- a/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_parameters.cfg +++ b/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile schizosaccharomyces_pombe_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile schizosaccharomyces_pombe_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/scyliorhinus/scyliorhinus_parameters.cfg b/config/species/scyliorhinus/scyliorhinus_parameters.cfg index 2c9d9b5d..c049cb4f 100644 --- a/config/species/scyliorhinus/scyliorhinus_parameters.cfg +++ b/config/species/scyliorhinus/scyliorhinus_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.15 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile scyliorhinus_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile scyliorhinus_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1 b/config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1 index a1c7b31d..131ec1d4 100644 --- a/config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1 +++ b/config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile catshark3_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile catshark3_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/sealamprey/sealamprey_parameters.cfg b/config/species/sealamprey/sealamprey_parameters.cfg index 565a0c4c..2b5b7ee4 100644 --- a/config/species/sealamprey/sealamprey_parameters.cfg +++ b/config/species/sealamprey/sealamprey_parameters.cfg @@ -9,7 +9,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -69,7 +69,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile sealamprey_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile sealamprey_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg b/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg index f3845c43..cc2108cc 100644 --- a/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg +++ b/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile strongylocentrotus_purpuratus_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile strongylocentrotus_purpuratus_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg b/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg index 80f963fc..47c46c58 100644 --- a/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg +++ b/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg @@ -9,7 +9,7 @@ #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.25 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.75 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.208 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile sulfolobus_solfataricus_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile sulfolobus_solfataricus_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_trans_shadow_bacterium.pbl b/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_trans_shadow_bacterium.pbl index 4167c3e4..9391a750 100644 --- a/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_trans_shadow_bacterium.pbl +++ b/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_trans_shadow_bacterium.pbl @@ -21,7 +21,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 3 diff --git a/config/species/template_prokaryotic/template_prokaryotic_parameters.cfg b/config/species/template_prokaryotic/template_prokaryotic_parameters.cfg index a905e739..1c87f69b 100644 --- a/config/species/template_prokaryotic/template_prokaryotic_parameters.cfg +++ b/config/species/template_prokaryotic/template_prokaryotic_parameters.cfg @@ -9,7 +9,7 @@ #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.25 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.75 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 2 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 2 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.067 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile template_prokaryotic_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile template_prokaryotic_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/template_prokaryotic/template_prokaryotic_trans_shadow_bacterium.pbl b/config/species/template_prokaryotic/template_prokaryotic_trans_shadow_bacterium.pbl index 4167c3e4..9391a750 100644 --- a/config/species/template_prokaryotic/template_prokaryotic_trans_shadow_bacterium.pbl +++ b/config/species/template_prokaryotic/template_prokaryotic_trans_shadow_bacterium.pbl @@ -21,7 +21,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 3 diff --git a/config/species/tetrahymena/tetrahymena_parameters.cfg b/config/species/tetrahymena/tetrahymena_parameters.cfg index ab99e895..5c3a4452 100644 --- a/config/species/tetrahymena/tetrahymena_parameters.cfg +++ b/config/species/tetrahymena/tetrahymena_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -63,7 +63,7 @@ keep_viterbi true # set to true if all Viterbi transcripts should be r # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile tetrahymena_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile tetrahymena_weightmatrix.txt # change this to your species if at all necessary # tetrahymena uses alternative translation table translation_table 6 diff --git a/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg b/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg index 6156ae22..c1e10bab 100644 --- a/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg +++ b/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg @@ -9,7 +9,7 @@ #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.3 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.43 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.169 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile thermoanaerobacter_tengcongensis_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile thermoanaerobacter_tengcongensis_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_trans_shadow_bacterium.pbl b/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_trans_shadow_bacterium.pbl index 64033dfb..45e2c372 100644 --- a/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_trans_shadow_bacterium.pbl +++ b/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_trans_shadow_bacterium.pbl @@ -21,7 +21,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 3 diff --git a/config/species/tomato/tomato_parameters.cfg b/config/species/tomato/tomato_parameters.cfg index 6ff9fe42..c9fdb3e5 100644 --- a/config/species/tomato/tomato_parameters.cfg +++ b/config/species/tomato/tomato_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 2 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 2 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.15 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.227 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile tomato_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile tomato_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/toxoplasma/toxoplasma_parameters.cfg b/config/species/toxoplasma/toxoplasma_parameters.cfg index a1670d64..bfcf8383 100644 --- a/config/species/toxoplasma/toxoplasma_parameters.cfg +++ b/config/species/toxoplasma/toxoplasma_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -55,7 +55,7 @@ UTR on /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 /Constant/amberprob 0.28 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -65,7 +65,7 @@ UTR on # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile toxoplasma_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile toxoplasma_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/toxoplasma/toxoplasma_trans_shadow_partial_utr.pbl b/config/species/toxoplasma/toxoplasma_trans_shadow_partial_utr.pbl index a52add1a..d08c64a3 100644 --- a/config/species/toxoplasma/toxoplasma_trans_shadow_partial_utr.pbl +++ b/config/species/toxoplasma/toxoplasma_trans_shadow_partial_utr.pbl @@ -91,7 +91,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 71 diff --git a/config/species/tribolium2012/tribolium2012_parameters.cfg b/config/species/tribolium2012/tribolium2012_parameters.cfg index d0306f39..eab4e2ff 100644 --- a/config/species/tribolium2012/tribolium2012_parameters.cfg +++ b/config/species/tribolium2012/tribolium2012_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -80,7 +80,7 @@ mea 0 # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig1 b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig1 index e0f2bdd1..704e864b 100644 --- a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig1 +++ b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig1 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -79,7 +79,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig2 b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig2 index e0f2bdd1..704e864b 100644 --- a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig2 +++ b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig2 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -79,7 +79,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig3 b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig3 index de06c9eb..a738063c 100644 --- a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig3 +++ b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig3 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -80,7 +80,7 @@ mea 1 # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig4 b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig4 index 665a6ce5..d033d213 100644 --- a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig4 +++ b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig4 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig5 b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig5 index 665a6ce5..d033d213 100644 --- a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig5 +++ b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig5 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig6 b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig6 index 665a6ce5..d033d213 100644 --- a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig6 +++ b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig6 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig7 b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig7 index 665a6ce5..d033d213 100644 --- a/config/species/tribolium2012/tribolium2012_parameters.cfg.orig7 +++ b/config/species/tribolium2012/tribolium2012_parameters.cfg.orig7 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile tribolium2012_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/tribolium2012/tribolium2012_trans_shadow_partial_utr.pbl b/config/species/tribolium2012/tribolium2012_trans_shadow_partial_utr.pbl index 71add6c6..a4f62679 100644 --- a/config/species/tribolium2012/tribolium2012_trans_shadow_partial_utr.pbl +++ b/config/species/tribolium2012/tribolium2012_trans_shadow_partial_utr.pbl @@ -90,7 +90,7 @@ # Terminal probabilities (a priori probs for a state ending at # the last position. -# only non-zero probabilities neccessary +# only non-zero probabilities necessary [Terminal] # number of states where terminating is possible 71 diff --git a/config/species/trichinella/trichinella_parameters.cfg b/config/species/trichinella/trichinella_parameters.cfg index 3d9b2dc1..087c9e7b 100644 --- a/config/species/trichinella/trichinella_parameters.cfg +++ b/config/species/trichinella/trichinella_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.154 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile trichinella_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile trichinella_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/ustilago/ustilago_parameters.cfg b/config/species/ustilago/ustilago_parameters.cfg index 7fc7d92a..58ca3ff4 100644 --- a/config/species/ustilago/ustilago_parameters.cfg +++ b/config/species/ustilago/ustilago_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS in the training set do not include the stop codon diff --git a/config/species/ustilago/ustilago_weightmatrix.txt b/config/species/ustilago/ustilago_weightmatrix.txt index f9640523..8c9c3abb 100644 --- a/config/species/ustilago/ustilago_weightmatrix.txt +++ b/config/species/ustilago/ustilago_weightmatrix.txt @@ -1,7 +1,7 @@ # # This file contains a matrix used for weighing the training sequences # when given an input sequence. Let z = (da, dc, dg, dt) be the vector -# containing the differences in the relative nukleotide frequencies of +# containing the differences in the relative nucleotide frequencies of # two sequences, the input sequence and a training sequence. # Then the training sequence has weight proportional to # diff --git a/config/species/ustilago_maydis/ustilago_maydis_parameters.cfg b/config/species/ustilago_maydis/ustilago_maydis_parameters.cfg index a888a54b..c3a45caf 100644 --- a/config/species/ustilago_maydis/ustilago_maydis_parameters.cfg +++ b/config/species/ustilago_maydis/ustilago_maydis_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile ustilago_maydis_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile ustilago_maydis_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_parameters.cfg b/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_parameters.cfg index 3d687906..29c886ec 100644 --- a/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_parameters.cfg +++ b/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 5 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 5 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.248 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile verticillium_albo_atrum1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile verticillium_albo_atrum1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg b/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg index b20ec202..380e31f0 100644 --- a/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg +++ b/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 3 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 3 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.282 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile verticillium_longisporum1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile verticillium_longisporum1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1 b/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1 index 9f53bdee..367bfe73 100644 --- a/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1 +++ b/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1 @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.282 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile verticillium_longisporum1_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile verticillium_longisporum1_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/volvox/volvox_parameters.cfg b/config/species/volvox/volvox_parameters.cfg index 6f2d22ac..fa8087ad 100644 --- a/config/species/volvox/volvox_parameters.cfg +++ b/config/species/volvox/volvox_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.262 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile volvox_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile volvox_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/wheat/wheat_parameters.cfg b/config/species/wheat/wheat_parameters.cfg index e6f9e778..b64ac1be 100644 --- a/config/species/wheat/wheat_parameters.cfg +++ b/config/species/wheat/wheat_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 500000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -56,7 +56,7 @@ UTR on # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.73 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.24375 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.297 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -68,7 +68,7 @@ UTR on # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile wheat_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile wheat_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/yarrowia_lipolytica/yarrowia_lipolytica_parameters.cfg b/config/species/yarrowia_lipolytica/yarrowia_lipolytica_parameters.cfg index eee43b82..f44a1df9 100644 --- a/config/species/yarrowia_lipolytica/yarrowia_lipolytica_parameters.cfg +++ b/config/species/yarrowia_lipolytica/yarrowia_lipolytica_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 200000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop codon (training and prediction) @@ -67,7 +67,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile yarrowia_lipolytica_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile yarrowia_lipolytica_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/config/species/zebrafish/zebrafish_parameters.cfg b/config/species/zebrafish/zebrafish_parameters.cfg index 6f334f47..0fbb7a29 100644 --- a/config/species/zebrafish/zebrafish_parameters.cfg +++ b/config/species/zebrafish/zebrafish_parameters.cfg @@ -7,7 +7,7 @@ # # Properties for augustus #------------------------------------ -/augustus/verbosity 3 # 0-3, 0: only print the neccessary +/augustus/verbosity 3 # 0-3, 0: only print the necessary maxDNAPieceSize 1000000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS true # make this 'true' if the CDS does not include the stop codon (training and prediction) @@ -58,7 +58,7 @@ UTR off # predict untranslated regions /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.30 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.50 # States the minimal and maximal percentage of c or g -/Constant/decomp_num_steps 2 # I recomment keeping this to 1 for most species. +/Constant/decomp_num_steps 2 # I recommend keeping this to 1 for most species. /Constant/min_coding_len 201 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.18 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid @@ -70,7 +70,7 @@ UTR off # predict untranslated regions # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) -/BaseCount/weightMatrixFile zebrafish_weightmatrix.txt # change this to your species if at all neccessary +/BaseCount/weightMatrixFile zebrafish_weightmatrix.txt # change this to your species if at all necessary # Properties for IGenicModel # ---------------------------- diff --git a/docs/CDS.sp.README b/docs/CDS.sp.README index 558f34b3..c347de69 100644 --- a/docs/CDS.sp.README +++ b/docs/CDS.sp.README @@ -5,6 +5,6 @@ for T in 0 1 2 3 4 5 6 7; do done The graph shows the posterior probability reported in the 6th column of the augustus output gff file versus the actual fraction of exons (CDS) that -match the reference annotation (RefSeq). The esimated curves for t=5,6,7 are not reliable for high posterior probabilities as they occurr too rarely. +match the reference annotation (RefSeq). The estimated curves for t=5,6,7 are not reliable for high posterior probabilities as they occur too rarely. For large temperatures exons with high posterior probability become increasingly rare. We recommend t=3 as it comes relatively close to the ideal curve, -the diagonal, for the most relavant range of posterior probabilities. +the diagonal, for the most relevant range of posterior probabilities. diff --git a/docs/espoca/README b/docs/espoca/README index b159ce49..bf6a7492 100644 --- a/docs/espoca/README +++ b/docs/espoca/README @@ -2,7 +2,7 @@ ESPOCA - Estimate Selective Pressure on Codon Alignments This directory contains example input files: example.fa codon alignment file in multi fasta format -tree.nwk phylogenetik tree file in newick format with branch length +tree.nwk phylogenetic tree file in newick format with branch length Example Command: @@ -21,7 +21,7 @@ Output: # 4. Pr(w>1) probability of omega > 1 at alipos (*: Pr(w>1) > 0.90, **: Pr(w>1) > 0.95) # 5. post_mean posterior mean estimate of omega at ali_pos # 6. SE_for_w standard deviation of omega at ali_pos -# 7. num_subst number of subsitution calculated by the Fitch algorithm +# 7. num_subst number of substitution calculated by the Fitch algorithm ali_pos ref_pos AS_ref Pr(w>1) post_mean +- SE_for_w num_subst 0 0 M 0.249188 0.814206 +- 0.362779 0 diff --git a/docs/tutorial-cgp/results/aug_rnaseq/bosTau8.gff b/docs/tutorial-cgp/results/aug_rnaseq/bosTau8.gff index e5950fd1..ace47fe9 100644 --- a/docs/tutorial-cgp/results/aug_rnaseq/bosTau8.gff +++ b/docs/tutorial-cgp/results/aug_rnaseq/bosTau8.gff @@ -6,7 +6,7 @@ # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. # Sources of extrinsic information: M RM -# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... +# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... # human version. Using default transition matrix. # Looks like ../genomes/bosTau8.fa is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. diff --git a/docs/tutorial-cgp/results/aug_rnaseq/canFam3.gff b/docs/tutorial-cgp/results/aug_rnaseq/canFam3.gff index 354bea61..eb9ba322 100644 --- a/docs/tutorial-cgp/results/aug_rnaseq/canFam3.gff +++ b/docs/tutorial-cgp/results/aug_rnaseq/canFam3.gff @@ -6,7 +6,7 @@ # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. # Sources of extrinsic information: M RM -# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... +# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... # human version. Using default transition matrix. # Looks like ../genomes/canFam3.fa is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. diff --git a/docs/tutorial-cgp/results/aug_rnaseq/galGal4.gff b/docs/tutorial-cgp/results/aug_rnaseq/galGal4.gff index 3f26302d..412a0ece 100644 --- a/docs/tutorial-cgp/results/aug_rnaseq/galGal4.gff +++ b/docs/tutorial-cgp/results/aug_rnaseq/galGal4.gff @@ -12,7 +12,7 @@ # Setting UTRpart local malus: 0.985 # reading in the file ../hints/galGal4.hints.gff ... # Have extrinsic information about 1 sequences (in the specified range). -# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... +# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... # human version. Using species specific transition matrix: /home/mario/augustus/git/Augustus/config/species/human/human_trans_shadow_partial_utr.pbl # Looks like ../genomes/galGal4.fa is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. diff --git a/docs/tutorial-cgp/results/aug_rnaseq/hg38.gff b/docs/tutorial-cgp/results/aug_rnaseq/hg38.gff index 6d196e07..b39c3e0e 100644 --- a/docs/tutorial-cgp/results/aug_rnaseq/hg38.gff +++ b/docs/tutorial-cgp/results/aug_rnaseq/hg38.gff @@ -12,7 +12,7 @@ # Setting UTRpart local malus: 0.985 # reading in the file ../hints/hg38.hints.gff ... # Have extrinsic information about 1 sequences (in the specified range). -# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... +# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... # human version. Using species specific transition matrix: /home/mario/augustus/git/Augustus/config/species/human/human_trans_shadow_partial_utr.pbl # Looks like ../genomes/hg38.fa is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. diff --git a/docs/tutorial-cgp/results/aug_rnaseq/mm10.gff b/docs/tutorial-cgp/results/aug_rnaseq/mm10.gff index 523e8def..aa71f229 100644 --- a/docs/tutorial-cgp/results/aug_rnaseq/mm10.gff +++ b/docs/tutorial-cgp/results/aug_rnaseq/mm10.gff @@ -12,7 +12,7 @@ # Setting UTRpart local malus: 0.985 # reading in the file ../hints/mm10.hints.gff ... # Have extrinsic information about 1 sequences (in the specified range). -# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... +# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... # human version. Using species specific transition matrix: /home/mario/augustus/git/Augustus/config/species/human/human_trans_shadow_partial_utr.pbl # Looks like ../genomes/mm10.fa is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. diff --git a/docs/tutorial-cgp/results/aug_rnaseq/monDom5.gff b/docs/tutorial-cgp/results/aug_rnaseq/monDom5.gff index a64d0f73..161bbaa2 100644 --- a/docs/tutorial-cgp/results/aug_rnaseq/monDom5.gff +++ b/docs/tutorial-cgp/results/aug_rnaseq/monDom5.gff @@ -6,7 +6,7 @@ # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. # Sources of extrinsic information: M RM -# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... +# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... # human version. Using default transition matrix. # Looks like ../genomes/monDom5.fa is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. diff --git a/docs/tutorial-cgp/results/aug_rnaseq/rheMac3.gff b/docs/tutorial-cgp/results/aug_rnaseq/rheMac3.gff index 277992a3..5128d18c 100644 --- a/docs/tutorial-cgp/results/aug_rnaseq/rheMac3.gff +++ b/docs/tutorial-cgp/results/aug_rnaseq/rheMac3.gff @@ -12,7 +12,7 @@ # Setting UTRpart local malus: 0.985 # reading in the file ../hints/rheMac3.hints.gff ... # Have extrinsic information about 1 sequences (in the specified range). -# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... +# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... # human version. Using species specific transition matrix: /home/mario/augustus/git/Augustus/config/species/human/human_trans_shadow_partial_utr.pbl # Looks like ../genomes/rheMac3.fa is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. diff --git a/docs/tutorial-cgp/results/aug_rnaseq/rn6.gff b/docs/tutorial-cgp/results/aug_rnaseq/rn6.gff index 3e9a94be..da7b39b8 100644 --- a/docs/tutorial-cgp/results/aug_rnaseq/rn6.gff +++ b/docs/tutorial-cgp/results/aug_rnaseq/rn6.gff @@ -6,7 +6,7 @@ # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. # Sources of extrinsic information: M RM -# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... +# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ... # human version. Using default transition matrix. # Looks like ../genomes/rn6.fa is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. diff --git a/docs/tutorial/results/augustus-ppx.gff b/docs/tutorial/results/augustus-ppx.gff index a266a20f..2bfdc53a 100644 --- a/docs/tutorial/results/augustus-ppx.gff +++ b/docs/tutorial/results/augustus-ppx.gff @@ -6,7 +6,7 @@ # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. -# Initialising the parameters ... +# Initializing the parameters ... # Using protein profile unknown # --[8..1336]--> unknown_A (9) <--[16..88]--> unknown_B (7) <--[19..46]--> unknown_D (8) <--[0..1]--> unknown_E (10) <--[2..42]--> unknown_F (10) <--[9..128]--> unknown_G (11) <--[16..74]--> unknown_H (16) <--[10..54]--> unknown_I (8) <--[8..29]--> unknown_J (13) <--[8..42]--> unknown_K (15) <--[1..3]--> unknown_L (12) <--[6..15]--> unknown_M (13) <---- # human version. Use default transition matrix. diff --git a/docs/tutorial/results/augustus.abinitio.gff b/docs/tutorial/results/augustus.abinitio.gff index df210553..7c518cf6 100644 --- a/docs/tutorial/results/augustus.abinitio.gff +++ b/docs/tutorial/results/augustus.abinitio.gff @@ -5,7 +5,7 @@ # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. -# Initialising the parameters ... +# Initializing the parameters ... # fly version. Use default transition matrix. # Looks like chr2R.fa is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. diff --git a/docs/tutorial/results/augustus.hints.gff b/docs/tutorial/results/augustus.hints.gff index 7b364c48..c64457b6 100644 --- a/docs/tutorial/results/augustus.hints.gff +++ b/docs/tutorial/results/augustus.hints.gff @@ -9,7 +9,7 @@ # Setting UTRpart local malus: 0.96 # Sources of extrinsic information: M E W # Have extrinsic information about 1 sequences (in the specified range). -# Initialising the parameters ... +# Initializing the parameters ... # fly version. Use default transition matrix. # Looks like chr2R.fa is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. diff --git a/docs/tutorial/results/output-abinitio.gff b/docs/tutorial/results/output-abinitio.gff index d45fec7e..aabb322c 100644 --- a/docs/tutorial/results/output-abinitio.gff +++ b/docs/tutorial/results/output-abinitio.gff @@ -6,7 +6,7 @@ # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. -# Initialising the parameters ... +# Initializing the parameters ... # human version. Use default transition matrix. # Looks like chr4.103M.fa is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. diff --git a/docs/tutorial/results/output.gff b/docs/tutorial/results/output.gff index 51c6f225..a6609534 100644 --- a/docs/tutorial/results/output.gff +++ b/docs/tutorial/results/output.gff @@ -6,7 +6,7 @@ # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. -# Initialising the parameters ... +# Initializing the parameters ... # Using protein profile unknown # --[8..1336]--> unknown_A (9) <--[16..88]--> unknown_B (7) <--[19..46]--> unknown_D (8) <--[0..1]--> unknown_E (10) <--[2..42]--> unknown_F (10) <--[9..128]--> unknown_G (11) <--[16..74]--> unknown_H (16) <--[9..54]--> unknown_I (8) <--[8..29]--> unknown_J (13) <--[8..42]--> unknown_K (15) <--[1..3]--> unknown_L (12) <--[6..15]--> unknown_M (13) <---- # human version. Use default transition matrix. diff --git a/docs/tutorial/scipio.html b/docs/tutorial/scipio.html index 851020ca..f432c2c1 100644 --- a/docs/tutorial/scipio.html +++ b/docs/tutorial/scipio.html @@ -39,7 +39,7 @@

    Using Scipio to create a (training) set of gene structures

    the proteins encoded by the genome (e.g. >90% similarity). One use case is the migration of gene structures from one assembly to another assembly. Another use case is the identification of exon coordinates for protein of the same species as the genome when the gene structures (GFF) is not available (anymore). A third use case is the mapping of protein sequences from a related known species to a new species, e.g. from human to Orangutan. Scipio is well-suited for draft assemblies with short -contigs, as it is assemblying alignments of proteins where different fragments match different contigs. +contigs, as it is assembling alignments of proteins where different fragments match different contigs.

    1. Run Scipio

    diff --git a/docs/tutorial/training.html b/docs/tutorial/training.html index ccbc2e0f..0f9a56a5 100644 --- a/docs/tutorial/training.html +++ b/docs/tutorial/training.html @@ -375,7 +375,7 @@

    4. RUN THE SCRIPT optimize_augustus.pl

    in the case of Tetrahymena, where taa and tag are coding for glutamine (Q).

    -Choose the translation table number accoding to this table. translation_table=1 is +Choose the translation table number according to this table. translation_table=1 is the default value and the standard with stop codons taa, tga, tag. If you have a species with the standard genetic code you don't have to do anything. In case your species' code is not covered by this table send us a note with the string of 64 one-letter amino acid codes in the codon order below.

    diff --git a/docs/tutorial2015/index.html b/docs/tutorial2015/index.html index 37f99d86..824eae57 100644 --- a/docs/tutorial2015/index.html +++ b/docs/tutorial2015/index.html @@ -66,7 +66,7 @@

    Exercise 1: Compile a Training Set

    to estimate the parameters of gene finders. We will here go through option 6. We assume that we have RNA-Seq data only and no substantial homology data. We will reuse an existing parameter set for AUGUSTUS.
      -
    1. Follow the tutorial on "Iteratative Training Set Construction" +
    2. Follow the tutorial on "Iterative Training Set Construction" and create a training set genes.gb.
    3. Partition genes.gb into a training set and a holdout test setas described in 1.2 Split gene structure set....
    diff --git a/docs/tutorial2015/ittrain.html b/docs/tutorial2015/ittrain.html index eb8e3ca8..abf46210 100644 --- a/docs/tutorial2015/ittrain.html +++ b/docs/tutorial2015/ittrain.html @@ -268,7 +268,7 @@

    5. Create a training set

    and to include genes in the "intergenic" region. The choice of the parameter max-size-of-gene-flanking-DNA is important for several reasons.
      -
    • The flanking region should be large enough to allow a prepresentative estimate of non coding regions. +
    • The flanking region should be large enough to allow a representative estimate of non coding regions. When the GFF file only contains CDS, then part of the flanking regions are UTR and may not be representative of intergenic region (e.g. CpG islands in vertebrates).
    • Usually the gff file is not complete and genes are missing from it. In that case the flanking regions may contain genic regions diff --git a/docs/tutorial2015/prediction.html b/docs/tutorial2015/prediction.html index cbc07756..bd44f689 100644 --- a/docs/tutorial2015/prediction.html +++ b/docs/tutorial2015/prediction.html @@ -186,7 +186,7 @@

      3.1 From ESTs

      cat est.psl | filterPSL.pl --best --minCover=80 > est.f.psl
      est.f.psl now only contains for each query -the best alginment(s) and that only if it covers at least 80% of the query length. +the best alignment(s) and that only if it covers at least 80% of the query length. This reduces the number of alignments: 
       wc -l est.psl est.f.psl
diff --git a/docs/tutorial2015/results/aug.nasonia.1-1M.gff b/docs/tutorial2015/results/aug.nasonia.1-1M.gff
index 0624c79d..542b1bf1 100644
--- a/docs/tutorial2015/results/aug.nasonia.1-1M.gff
+++ b/docs/tutorial2015/results/aug.nasonia.1-1M.gff
@@ -6,7 +6,7 @@
 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
 # No extrinsic information on sequences given.
 # Sources of extrinsic information: M RM 
-# Initialising the parameters using config directory /home/mario/augustus/trunks/config/ ...
+# Initializing the parameters using config directory /home/mario/augustus/trunks/config/ ...
 # nasonia version. Using default transition matrix.
 # Looks like chr2L.sm.fa is in fasta format.
 # We have hints for 0 sequences and for 0 of the sequences in the input set.
diff --git a/docs/tutorial2015/results/aug.nasonia.hints.gff b/docs/tutorial2015/results/aug.nasonia.hints.gff
index 81fe82df..f2bc1d85 100644
--- a/docs/tutorial2015/results/aug.nasonia.hints.gff
+++ b/docs/tutorial2015/results/aug.nasonia.hints.gff
@@ -12,7 +12,7 @@
 # Setting UTRpart local malus: 0.985
 # reading in the file hints.gff ...
 # Have extrinsic information about 1 sequences (in the specified range). 
-# Initialising the parameters using config directory /home/mario/augustus/trunks/config/ ...
+# Initializing the parameters using config directory /home/mario/augustus/trunks/config/ ...
 # nasonia version. Using default transition matrix.
 # start gene g1
 chr2L	AUGUSTUS	gene	6774	9276	0.44	+	.	g1
diff --git a/docs/tutorial2015/results/aug.tomato.1-1M.gff b/docs/tutorial2015/results/aug.tomato.1-1M.gff
index e995a522..ff4c5e1b 100644
--- a/docs/tutorial2015/results/aug.tomato.1-1M.gff
+++ b/docs/tutorial2015/results/aug.tomato.1-1M.gff
@@ -6,7 +6,7 @@
 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
 # No extrinsic information on sequences given.
 # Sources of extrinsic information: M RM 
-# Initialising the parameters using config directory /home/mario/augustus/trunks/config/ ...
+# Initializing the parameters using config directory /home/mario/augustus/trunks/config/ ...
 # tomato version. Using default transition matrix.
 # Looks like chr2L.sm.fa is in fasta format.
 # We have hints for 0 sequences and for 0 of the sequences in the input set.
diff --git a/docs/tutorial2015/results/aug.zebrafish.1-1M.gff b/docs/tutorial2015/results/aug.zebrafish.1-1M.gff
index ae8fd7a6..02155aa4 100644
--- a/docs/tutorial2015/results/aug.zebrafish.1-1M.gff
+++ b/docs/tutorial2015/results/aug.zebrafish.1-1M.gff
@@ -6,7 +6,7 @@
 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
 # No extrinsic information on sequences given.
 # Sources of extrinsic information: M RM 
-# Initialising the parameters using config directory /home/mario/augustus/trunks/config/ ...
+# Initializing the parameters using config directory /home/mario/augustus/trunks/config/ ...
 # zebrafish version. Using default transition matrix.
 # admissible start codons and their probabilities: ATG(0.999), CTG(0.000667), TTG(0)
 # Looks like chr2L.sm.fa is in fasta format.
diff --git a/docs/tutorial2015/results/firsttest.out b/docs/tutorial2015/results/firsttest.out
index 6d1d8bdb..5fd08d8c 100644
--- a/docs/tutorial2015/results/firsttest.out
+++ b/docs/tutorial2015/results/firsttest.out
@@ -5,7 +5,7 @@
 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
 # No extrinsic information on sequences given.
-# Initialising the parameters using config directory /home/mario/augustus/trunks/config/ ...
+# Initializing the parameters using config directory /home/mario/augustus/trunks/config/ ...
 # bug version. Using default transition matrix.
 # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
 # Looks like genes.gb.test is in genbank format. Augustus uses the annotation for evaluation of accuracy.
diff --git a/docs/tutorial2015/training.html b/docs/tutorial2015/training.html
index 84035952..2d6ba5d8 100644
--- a/docs/tutorial2015/training.html
+++ b/docs/tutorial2015/training.html
@@ -376,7 +376,7 @@ 
      4. RUN THE SCRIPT optimize_augustus.pl
      
 in the case of Tetrahymena, where taa and tag are coding for glutamine (Q).
 
 
      
-Choose the translation table number accoding to this table. translation_table=1 is 
+Choose the translation table number according to this table. translation_table=1 is 
 the default value and the standard with stop codons taa, tga, tag. If you have a species with the standard genetic code you don't have to do anything.
 In case your species' code is not covered by this table send us a note with the string of 64 one-letter amino acid codes in the codon order below.
 
      
diff --git a/docs/tutorial2018/BRAKER_v2.0.4+/align2hints.pl b/docs/tutorial2018/BRAKER_v2.0.4+/align2hints.pl
index cdc63562..8af67f9d 100644
--- a/docs/tutorial2018/BRAKER_v2.0.4+/align2hints.pl
+++ b/docs/tutorial2018/BRAKER_v2.0.4+/align2hints.pl
@@ -11,7 +11,7 @@
 #                                                                                                  #
 # Release date: February xx 2018                                                                   #
 #                                                                                                  #
-# This script is under the Artistic Licence                                                        #
+# This script is under the Artistic License                                                        #
 # (http://www.opensource.org/licenses/artistic-license.php)                                        #
 #                                                                                                  #
 # Usage:                                                                                           #
diff --git a/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl b/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl
index 51b3614b..d3010428 100644
--- a/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl
+++ b/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl
@@ -11,7 +11,7 @@
 #                                                                                                  #
 # Release date: February 9th 2018                                                                  #
 #                                                                                                  #
-# This script is under the Artistic Licence                                                        #
+# This script is under the Artistic License                                                        #
 # (http://www.opensource.org/licenses/artistic-license.php)                                        #
 #                                                                                                  #
 ####################################################################################################
@@ -2504,9 +2504,9 @@ sub training{
 
             # decide on whether to keep CRF parameters
             if($target_2>$target_3){
-                print LOG "\# ".(localtime).": CRF performance is worse than HMM performance, reverting to usage of HMM paramters.\n";
+                print LOG "\# ".(localtime).": CRF performance is worse than HMM performance, reverting to usage of HMM parameters.\n";
             }else{
-                print LOG "\# ".(localtime).": CRF performance is better than HMM performance, keeping CRF paramters.\n";
+                print LOG "\# ".(localtime).": CRF performance is better than HMM performance, keeping CRF parameters.\n";
             }
             # cp config files
             print LOG "\# ".(localtime).": Copying parameter files to $species*.CRF\n";
diff --git a/docs/tutorial2018/BRAKER_v2.0.4+/filterGenemark.pl b/docs/tutorial2018/BRAKER_v2.0.4+/filterGenemark.pl
index 224a099b..6502f026 100644
--- a/docs/tutorial2018/BRAKER_v2.0.4+/filterGenemark.pl
+++ b/docs/tutorial2018/BRAKER_v2.0.4+/filterGenemark.pl
@@ -14,7 +14,7 @@
 # First release date: January 7th 2015                                                             #
 # Last update: February 10th 2016
 #                                                                                                  #
-# This script is under the Artistic Licence                                                        #
+# This script is under the Artistic License                                                        #
 # (http://www.opensource.org/licenses/artistic-license.php)                                        #
 #                                                                                                  #
 #################################################################################################### 
diff --git a/docs/tutorial2018/BRAKER_v2.0.4+/filterIntronsFindStrand.pl b/docs/tutorial2018/BRAKER_v2.0.4+/filterIntronsFindStrand.pl
index 54c4338a..fecbf652 100644
--- a/docs/tutorial2018/BRAKER_v2.0.4+/filterIntronsFindStrand.pl
+++ b/docs/tutorial2018/BRAKER_v2.0.4+/filterIntronsFindStrand.pl
@@ -11,7 +11,7 @@
 #                                                                                                  #
 # Release date: January 7th 2015                                                                   #
 #                                                                                                  #
-# This script is under the Artistic Licence                                                        #
+# This script is under the Artistic License                                                        #
 # (http://www.opensource.org/licenses/artistic-license.php)                                        #
 #                                                                                                  #
 ####################################################################################################
diff --git a/docs/tutorial2018/BRAKER_v2.0.4+/licence.txt b/docs/tutorial2018/BRAKER_v2.0.4+/licence.txt
index 6ddf1061..7315b9c4 100644
--- a/docs/tutorial2018/BRAKER_v2.0.4+/licence.txt
+++ b/docs/tutorial2018/BRAKER_v2.0.4+/licence.txt
@@ -1,4 +1,4 @@
-Artistic Licence (http://www.opensource.org/licenses/artistic-license.php)
+Artistic License (http://www.opensource.org/licenses/artistic-license.php)
 
 Preamble
 
diff --git a/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl b/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl
index 347440c7..d203ede1 100644
--- a/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl
+++ b/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl
@@ -11,7 +11,7 @@
 #                                                                                                  #
 # Release date: July 11th 2017                                                                     #
 #                                                                                                  #
-# This script is under the Artistic Licence                                                        #
+# This script is under the Artistic License                                                        #
 # (http://www.opensource.org/licenses/artistic-license.php)                                        #
 #                                                                                                  #
 #################################################################################################### 
diff --git a/docs/tutorial2018/README_augustus.TXT b/docs/tutorial2018/README_augustus.TXT
index 85f2e794..065d5483 100644
--- a/docs/tutorial2018/README_augustus.TXT
+++ b/docs/tutorial2018/README_augustus.TXT
@@ -26,7 +26,7 @@
   10. MEA: USING THE MAXIMUM EXPECTED ACCURACY APPROACH
   11. CONTACT ME
   12. REFERENCES
-  13. LICENCES
+  13. LICENSES
 
               1. INTRODUCTION
               ---------------
@@ -721,7 +721,7 @@ HS04636	blat2hints	exonpart	500	599	.	+	.	priority=2; source=E
 HS04636	blat2hints	intron		550	650	.	+	.	priority=5; source=mRNA
 
 When two hints or hint groups contradict each other then the hints with the lower priority number
-are ignored. This is especially usefull if for a genome several sources of hints are available,
+are ignored. This is especially useful if for a genome several sources of hints are available,
 where one source should be trusted when in doubt. For example, the rhesus macaque currently has few native ESTs
 but human ESTs often also align to rhesus. Giving the hints from native ESTs a higher priority means
 that AUGUSTUS uses only them for genes with support by native ESTs and uses the alien EST alignments
@@ -965,7 +965,7 @@ Mario Stanke and Stephan Waack (2003),
 Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225 
 
 
-              13. LICENCES
+              13. LICENSES
               ------------
 
 All source code, i.e.
@@ -973,4 +973,4 @@ All source code, i.e.
   - the scripts (scripts/*.pl)
   - the auxiliary programs (auxprogs/)
   - the tree-parser (src/scanner,src/parser)
-are under the Artistic Licence (see src/LICENCE.TXT).
+are under the Artistic License (see src/LICENSE.TXT).
diff --git a/docs/tutorial2018/data/augustus_ab_initio.gff b/docs/tutorial2018/data/augustus_ab_initio.gff
index 6fcf0f08..334f1434 100644
--- a/docs/tutorial2018/data/augustus_ab_initio.gff
+++ b/docs/tutorial2018/data/augustus_ab_initio.gff
@@ -5,7 +5,7 @@
 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
 # No extrinsic information on sequences given.
-# Initialising the parameters ...
+# Initializing the parameters ...
 # o.tauri version. Using default transition matrix.
 # Looks like masking/genome.fa.softmasked is in fasta format.
 # We have hints for 0 sequences and for 0 of the sequences in the input set.
diff --git a/docs/tutorial2018/index.html b/docs/tutorial2018/index.html
index 2811393f..10c72ba8 100644
--- a/docs/tutorial2018/index.html
+++ b/docs/tutorial2018/index.html
@@ -12,7 +12,7 @@ 
      Using BRAKER2 and AUGUSTUS
      
 
      General remarks
      
 
 
        
-  
      •  This tutorial is designed in a way that persons with no exprience in Linux should be able to follow. In case someone gets bored, he or she can try to get the code of this tutorial on his own laptop running.
+  
      •  This tutorial is designed in a way that persons with no experience in Linux should be able to follow. In case someone gets bored, he or she can try to get the code of this tutorial on his own laptop running.
   
      •  Here some manuals:
   
          
     
        •  AUGUSTUS readme
@@ -164,7 +164,7 @@ 
          1. Repeat-mask the genome 
          
 RepeatScout -sequence data/genome.fa -output masking/genome.repseq.fa -freq masking/genome.freq   # takes ~30s
      -The file masking/genome.freq contains a list of ostensibe repeat sequences. +The file masking/genome.freq contains a list of ostensible repeat sequences. 
       head -n 100 masking/genome.freq
@@ -360,7 +360,7 @@ 
      3. Gene prediction 
      
 The options in the BRAKE call have the follownig meanings:
 
        
   
      •  --species: The name of the species on which we carry out our gene prediction. 
         
-  The parameters AUGUSTUS infers from the training data and uses to parametrize its internal model for the gene prediciton is located in AUGUSTUS_CONFIG_PATH/species/[value of --species]. The term "species" is used in this option although AUGUSTUS can also be used for gene predictions on different strains of the same species.
+  The parameters AUGUSTUS infers from the training data and uses to parametrize its internal model for the gene prediction is located in AUGUSTUS_CONFIG_PATH/species/[value of --species]. The term "species" is used in this option although AUGUSTUS can also be used for gene predictions on different strains of the same species.
   
      •  --genome: The genomic data on which the gene prediction is carried out.
   
      •  --bam: The BAM file containign the aligned RNA-seq reads used for inference of the training genes by GeneMark and as hints for the gene prediction by AUGUSTUS
   
      •  --softmasking: Flag indicating that the genome is softmasked. 
        
@@ -369,7 +369,7 @@ 
        3. Gene prediction 
        
   One should not use the parameters AUGUSTUS infers without optimization to generate a gene set used in a scientific project. We skip optimization here because it is very time-consuming
   
      •  --cores: The number of cores used by BRAKER and AUGUSTUS. 
        
    To reduce running time, once can increase the number of cores. Nevertheless, for this session this is probably not advisable as the genotoul server only has 32 cores. 
-  
      •  --AUGUSTUS_SCRIPTS_PATH, --AUGUSTUS_BIN_PATH, --AUGUSTUS_CONFIG_PATH: These pathes specify where to find various files and executables. 
        
+  
      •  --AUGUSTUS_SCRIPTS_PATH, --AUGUSTUS_BIN_PATH, --AUGUSTUS_CONFIG_PATH: These paths specify where to find various files and executables. 
        
   When you install BRAKER and AUGUSTUS on a computer for which you have administrator rights, you very probably will not need to set these paths.
 
      
 
      
diff --git a/examples/profile/chr1.161M.gff b/examples/profile/chr1.161M.gff
index a4290b49..36c210dc 100644
--- a/examples/profile/chr1.161M.gff
+++ b/examples/profile/chr1.161M.gff
@@ -8,7 +8,7 @@
 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
 # No extrinsic information on sequences given.
-# Initialising the parameters ...
+# Initializing the parameters ...
 # Using protein profile HSP70
 # --[0..159]--> PF00012.13_A (30) <--[0..3]--> PF00012.13_B (33) <--[0..7]--> PF00012.13_C (13) <--[13..24]--> PF00012.13_D (75) <--[1..13]--> PF00012.13_E (21) <--[10..20]--> PF00012.13_F (12) <--[0..18]--> PF00012.13_G (11) <--[3..4]--> PF00012.13_H (27) <--[0..2]--> PF00012.13_I (13) <--[1..8]--> PF00012.13_J (34) <--[5..20]--> PF00012.13_K (26) <--[0..1]--> PF00012.13_L (26) <--[0..8]--> PF00012.13_M (39) <--[0..1]--> PF00012.13_N (35) <--[0..11]--> PF00012.13_O (33) <--[0..1]--> PF00012.13_P (15) <--[0..1]--> PF00012.13_Q (46) <--[34,...]--
 # human version. Use default transition matrix.
diff --git a/include/consensus.hh b/include/consensus.hh
index 8b814f84..865befa2 100644
--- a/include/consensus.hh
+++ b/include/consensus.hh
@@ -40,7 +40,7 @@ typedef struct histogram_data{
   vector mean_neighbours;
   int f_value;
   float mean_value;
-  vector position_of_occurence;
+  vector position_of_occurrence;
 } histogram_data;
 
 
@@ -52,10 +52,10 @@ class consensus{
    * no_iterations specifies the number of consensus patterns we need to store for the output
    * delta is used to calculate whether a certain string is relevant or not
    * p_value is the threshold used to identify the significant strings
-   * powers is the array used to store the powers 4 for caculating the character to int conversion and vice versa
-   * tpm is the transition probabiliry matrix
+   * powers is the array used to store the powers 4 for calculating the character to int conversion and vice versa
+   * tpm is the transition probability matrix
    * var is the vector of structure sequence containing all the input sequences
-   * t_values is a flag array used to store the actuall frequencies of the patterns
+   * t_values is a flag array used to store the actual frequencies of the patterns
    * f_values stores the actual frequencies of the patterns
    * back_probs store the background probabilities
    * significant_strings and relevant_strings store the significant and relevant strings respectively
@@ -72,9 +72,9 @@ class consensus{
   string analyse_pattern;
 
   /* consensus_data stores the consensus patterns as their corresponding integers
-   * final_list is a vector of struccture histogram_data
+   * final_list is a vector of structure histogram_data
    * max_string_length is the maximum length of the input string sequences
-   * max_freq is the maximum frequency of occurence at a particular position and is used to scale the histogram
+   * max_freq is the maximum frequency of occurrence at a particular position and is used to scale the histogram
    */
   vector consensus_data;
   vector final_list;
@@ -93,7 +93,7 @@ public:
   /* takes the file name to store the sequences
    */
   void set_file_name(string filename);
-  /* adds a particular string to consider for caculation
+  /* adds a particular string to consider for calculation
    */
   void add_string(string fileline);
   /* takes as input the pattern that we want to analyse and also the required parameters and does all the necessary 
@@ -107,7 +107,7 @@ public:
    */
   double poisThresh(int i, float p);
   /* calculates the poisson inverse between values a and b with threshold value p , number of iterations to perform n and 
-   * frequency of occurence i
+   * frequency of occurrence i
    */
   double poisInv(double a,double b, float p,int n,int i);
   /* starts the calculations
@@ -116,7 +116,7 @@ public:
   /* plots the histogram
    */
   void plot_histogram();
-  /* returns the consensus pattern and other reltaed information
+  /* returns the consensus pattern and other related information
    */
   vector get_consensus();
   /* prints the consensus pattern and other related information
@@ -128,7 +128,7 @@ public:
   /* returns n choose r
    */
   int nCr(int n, int r);
-  /* converts a character from A C G T to coresponding number value 0 1 2 3 respectively
+  /* converts a character from A C G T to corresponding number value 0 1 2 3 respectively
    */
   int char2num(char m);
   /* converts the numbers to corresponding character
@@ -139,7 +139,7 @@ public:
    * performing the calculations and the vector where the new neighbours is to be stored
    */
   void k_mismatch(int new_m, int old_m, int k, int length,Seq2Int s2i,vector &neighbours_index);
-  /* returns a vector containing k mismatch neighbours of pattern with interger value m and length as specified
+  /* returns a vector containing k mismatch neighbours of pattern with integer value m and length as specified
    */
   vector find_neighbours(int m,int k, int length);
 };
diff --git a/include/evaluation.hh b/include/evaluation.hh
index aaa059f0..f3abdc5a 100644
--- a/include/evaluation.hh
+++ b/include/evaluation.hh
@@ -135,7 +135,7 @@ private:
    */
 
   int numDataSets;
-  // nukleotide level
+  // nucleotide level
   int nukTPBK, nukFPBK, nukFPBKinside, nukFNBK;
            
   // exon level
diff --git a/include/exon_seg.hh b/include/exon_seg.hh
index a1833dcb..2d15ad54 100644
--- a/include/exon_seg.hh
+++ b/include/exon_seg.hh
@@ -29,7 +29,7 @@ const long int minus_infinity=LONG_MIN;
 const int maxcov =10000;
 #define NUMSTATES 4
 /* EXONP denotes positive exon EXONM denotes the negative exon INTRONJ and INTRONI denote the 
- * J and I lables of introns Together these four are teh states that we are considering
+ * J and I labels of introns Together these four are the states that we are considering
  * in our HMM
  */
 const int EXONP =0;
@@ -41,7 +41,7 @@ const int INTRONJ =3;
 const int STRANDP =0;
 const int STRANDM =1;
 const int STRANDB =2;
-/* pott_gamma denotes the gamma value that we will be using in calulating the
+/* pott_gamma denotes the gamma value that we will be using in calculating the
  * Pott's functionals
  */
 const int pott_gamma =1500;
@@ -49,10 +49,10 @@ const int pott_gamma =1500;
  * splice sites using the template matching technique
  */
 const int moving_window=70;
-/* The convergence limit that we use for calculating the labda values using the iterative technique
+/* The convergence limit that we use for calculating the lambda values using the iterative technique
  */
 const double convergence_limit=0.01;
-/* L stores the threshold betweeen introns and exons which we use when we try to estimate the
+/* L stores the threshold between introns and exons which we use when we try to estimate the
  * the distribution using the train_function which calculates the distribution using the exons
  * predicted from a gff file
  */
@@ -134,7 +134,7 @@ public:
   /* reads the file and stores it in the the object of the class dataset
    */
   void read_file(dataset &coverage_info,string filename);
-  /* it takes as input pointer to a 2-D vecctor, 
+  /* it takes as input pointer to a 2-D vector, 
    * the input dataset for a chromosome and
    * stores the emission probability values in it
    */
@@ -150,7 +150,7 @@ public:
   /* function to convert the state sequence into segments and also to store the avg coverage depth
    */
   vector< fragment > segment( vector state_seq,vector< vector< vector > > &input_set,int include_intron,int no_of_tracks );
-  /* This function takes input the averrage coverage depth and transforms them
+  /* This function takes input the average coverage depth and transforms them
    * into some usable form in the pott's functional
    */
   double pott_convert(double d);
@@ -166,7 +166,7 @@ public:
   vector cluster_exons(vector segments,int no_of_tracks);
 
   /* Takes the dataset, the name of output file and the threshold c and the ratio of complement 
-   * of the paramters(s) as input and makes the gff file
+   * of the parameters(s) as input and makes the gff file
    */
   void make_gff(dataset &coverage_info,string outputfile,int c,float s,string train_file,int flag_r,string bed_file,string augustus_hints,int chunksize);
   /* takes the dataset and vector of fragments as input and
diff --git a/include/extrinsicinfo.hh b/include/extrinsicinfo.hh
index 9582015b..ba9bd5b2 100644
--- a/include/extrinsicinfo.hh
+++ b/include/extrinsicinfo.hh
@@ -55,7 +55,7 @@ public:
 };
 
 /**
- * @brief Plan of individiual prediction steps with each a range and a set of hint groups turned on/off
+ * @brief Plan of individual prediction steps with each a range and a set of hint groups turned on/off
  * 
  * @author Mario Stanke
  */
@@ -235,10 +235,10 @@ public:
     int              seqlen;
     int              K; // block size for firstEnd and lastStart
     // firstEnd[t][k] holds an iterator to featureList[t] to the first element f in the list such that
-    // f->end >= k*K, where k>=0 and k ist such that k*K <= seqlen
+    // f->end >= k*K, where k>=0 and k is such that k*K <= seqlen
     list::iterator **firstEnd;
     // lastStart[t][k] holds an iterator to featureList[t] to the list such that all following list elements f have
-    // f->start > k*K, where k>=0 and k ist such that k*K <= seqlen 
+    // f->start > k*K, where k>=0 and k is such that k*K <= seqlen 
     list::iterator **lastStart;
     vector cumCovUTRpartPlus; // cumulative number of positions not covered by UTRpart hints on the plus strand
     vector cumCovUTRpartMinus; // cumulative number of positions not covered by UTRpart hints on the minus strand
@@ -258,7 +258,7 @@ private:
  */
 struct FeatureTypeInfo {
     FeatureTypeInfo(int numSources=1, double b=-1.0, double m=1.0, double lm=1.0) :
-	bonus(b), // -1 means not initialised
+	bonus(b), // -1 means not initialized
 	malus(m), // don't change anything unless we have at least searched 
 	localMalus(lm),
 	gradeclassbounds(numSources, vector()),
diff --git a/include/pp_profile.hh b/include/pp_profile.hh
index 0323d49b..504665ae 100644
--- a/include/pp_profile.hh
+++ b/include/pp_profile.hh
@@ -612,7 +612,7 @@ namespace PP {
 
     public:
 	// methods of class ProteinProfile
-	// initialise pattern from file 
+	// initialize pattern from file 
 	Profile(string filename);
 	
     
diff --git a/retraining.html b/retraining.html
index 0cc71009..5bcaeef1 100644
--- a/retraining.html
+++ b/retraining.html
@@ -178,7 +178,7 @@
 in the case of Tetrahymena, where taa and tag are coding for glutamine (Q).
 
 
-Choose the translation table number accoding to this table. translation_table=1 is 
+Choose the translation table number according to this table. translation_table=1 is 
 the default value and the standard with stop codons taa, tga, tag. If you have a species with the standard genetic code you don't have to do anything.
 In case your species' code is not covered by this table send us a note with the string of 64 one-letter amino acid codes in the codon order below.
 

      
diff --git a/scripts/README.autoAug b/scripts/README.autoAug
index 44b94165..355c20eb 100644
--- a/scripts/README.autoAug
+++ b/scripts/README.autoAug
@@ -41,7 +41,7 @@ TIP: Please manually/visually check the results of the pipeline, e.g. by loading
      The pipeline outputs files for tracks on a GBrowse. 
 
 WARNING: Please do not assume that you get the best possible results from a fully automatic pipeline.
-         Eykaryotic gene prediction is still a complex craft and some beasts are just different.
+         Eukaryotic gene prediction is still a complex craft and some beasts are just different.
 
 		2. System Overview
 		------------------
@@ -52,7 +52,7 @@ primarily within a MySQL database. The whole pipeline can take in the order of 1
 medium complete genome, so please be patient and consider using a compute cluster.
 If you happen to have a Sun Grid Engine available you can configure the pipeline to run in parallel
 and completely automatically. If you are using another cluster, the job scripts will be created and you 
-can then submit them manuall using your batch job submission system.
+can then submit them manually using your batch job submission system.
 
 		3. Software Components
 		-----------------------------------
@@ -84,18 +84,18 @@ shall be written in your startup script (like ~/.bashrc). Furthermore,
 all scripts of AUGUSTUS and PASA shall be executable. For 
 details see the documentations of AUGUSTUS and PASA.
 
-If you use PASA with GMAP instead of BLAT then please note that PASA is curently not fully compatible
+If you use PASA with GMAP instead of BLAT then please note that PASA is currently not fully compatible
 with GMAP versions after the version from 2007-09-28. If you use a newer GMAP version you might have to
  remove the "-S" option in the PASA script scripts/process_GMAP_alignments.pl so it says:
 gmap_setup -D gmap_db_dir -d $genome_db $genome_db
 (Although one user reported to us that GMAP-2012-04-07 needs exactly the -S tag!)
 
-Pay attention on how to configure PASA with MySQL! If you want to run PASA without root priviledges, you 
+Pay attention on how to configure PASA with MySQL! If you want to run PASA without root privileges, you 
 should first create a database for PASA (e.g. dbname-PASA, user priv > read and write), and then create
  a new database with name PASAspeciesname, where speciesname is the name you use in --species=speciesname. 
 
 Furthermore, if you are using a cluster, AUGUSTUS should be installed there as well. The 
-path to "augustus" should also be concated to the "PATH" in your cluster.  
+path to "augustus" should also be concatenated to the "PATH" in your cluster.  
 
 In case you are using a Sun Grid Engine and you want to use the option "noninteractive" (see section 6.),
 configure your ssh so that you can login on the cluster without having to type a password.
@@ -176,7 +176,7 @@ The keywords (such as genome) can be abbreviated (e.g. "ge") to the extend that
   This argument swithes the PASA function on for creating a training set of genes from the cDNA, default: off.
 
 --hints=hintsfile
-  hintsfile is a file with extrinsic evicence about the location and structure of genes, see documentation of AUGUSTUS.
+  hintsfile is a file with extrinsic evidence about the location and structure of genes, see documentation of AUGUSTUS.
 
 --estali=estfile
   cDNA alignments in PSL format (as generated by BLAT and GMAP) are used to construct UTRs
diff --git a/scripts/autoAugTrain.pl b/scripts/autoAugTrain.pl
index 940b2b0d..f9de397d 100755
--- a/scripts/autoAugTrain.pl
+++ b/scripts/autoAugTrain.pl
@@ -94,7 +94,7 @@ BEGIN
 	   'useexisting!' => \$useexisting
 	   );
 if ($flanking_DNA > 10000){
-    print "flanking_DNA larger than neccessary ($flanking_DNA). Resetting flanking_DNA to 10000.\n";
+    print "flanking_DNA larger than necessary ($flanking_DNA). Resetting flanking_DNA to 10000.\n";
     $flanking_DNA = 10000;
 }
 # show error information and stop the program if $species not specified
diff --git a/scripts/uniquePeptides.pl b/scripts/uniquePeptides.pl
index 6a9c59ac..f77e1602 100755
--- a/scripts/uniquePeptides.pl
+++ b/scripts/uniquePeptides.pl
@@ -2,7 +2,7 @@
 
 # Creates a fasta file with unique peptides from a fasta input file
 # where identical peptide match multiple positions. The first found 
-# peptide occurence is used for counting multiplicity.
+# peptide occurrence is used for counting multiplicity.
 # Input format fasta header examples:
 # >scaffold4083_450 [15866 - 17011]  (65.81)
 # >au14.g511.t1 (46.17)
diff --git a/scripts/writeResultsPage.pl b/scripts/writeResultsPage.pl
index 95af9439..ca485998 100755
--- a/scripts/writeResultsPage.pl
+++ b/scripts/writeResultsPage.pl
@@ -69,7 +69,7 @@
 }
 
 if($final == 1){
-## create a paramter folder in web-out folder
+## create a parameter folder in web-out folder
 if($projectID =~ m/^t/){
 	print STDOUT "writeResults.pl is called in training mode\nCollecting parameters\n";
 	my $projectWebOutParams = $wwwOut."/$projectID/$species";
@@ -162,7 +162,7 @@
 
 	## pack parameters
 	if(-e $AUGUSTUS_CONFIG_PATH."/species/$projectID/$projectID"."_parameters.cfg"){
-	    print STDOUT "Packing paramters...\n";
+	    print STDOUT "Packing parameters...\n";
 		$cmdStr = "cd $projectWebOutDir; tar -czvf parameters.tar.gz $species &> /dev/null;";
 		`$cmdStr`;
 	}
diff --git a/src/augustus.cc b/src/augustus.cc
index 388432a6..87b9e93f 100644
--- a/src/augustus.cc
+++ b/src/augustus.cc
@@ -1,6 +1,6 @@
 /**********************************************************************
  * file:    augustus.cc
- * licence: Artistic Licence, see file LICENCE.TXT or 
+ * license: Artistic License, see file LICENSE.TXT or 
  *          http://www.opensource.org/licenses/artistic-license.php
  *
  * authors: Mario Stanke, mario@gobics.de
@@ -115,7 +115,7 @@ int main( int argc, char* argv[] ){
 	Constant::init();
 	Gene::init();
 	GeneticCode::init();
-	setParameters(); // NOTE: need Constant and GeneticCode to be initialised first
+	setParameters(); // NOTE: need Constant and GeneticCode to be initialized first
 	StateModel::init();   // set global parameters of state models	  
 
 	if(Properties::hasProperty("trainFeatureFile"))
@@ -145,7 +145,7 @@ int main( int argc, char* argv[] ){
 	  cout << PREAMBLE << endl;
 	  
 	  /*
-	   * check for extrinsic information and initialise when existent
+	   * check for extrinsic information and initialize when existent
 	   */
 	  FeatureCollection extrinsicFeatures;
 	  const char *extrinsicfilename;
@@ -169,7 +169,7 @@ int main( int argc, char* argv[] ){
 	  }
 	  
 	  if (verbosity > 1) 
-	      cout << "# Initialising the parameters using config directory " << Properties::getProperty(CFGPATH_KEY) << " ..." << endl;
+	      cout << "# Initializing the parameters using config directory " << Properties::getProperty(CFGPATH_KEY) << " ..." << endl;
 	  BaseCount::init();
 	  PP::initConstants();
 	  NAMGene namgene; // creates and initializes the states
@@ -476,7 +476,7 @@ void setParameters(){
 	if (outdir != ""){
 	    outdir = expandHome(outdir);         // replace "~" by "$HOME"
 	    if(outdir[outdir.size()-1] != '/')
-		outdir += '/';                   // append slash if neccessary 
+		outdir += '/';                   // append slash if necessary 
 	    
 	    Properties::addProperty("/CompPred/outdir", outdir);
 	    // the directory actually exists? 
diff --git a/src/commontrain.cc b/src/commontrain.cc
index 9d7ea6f7..ffd80756 100644
--- a/src/commontrain.cc
+++ b/src/commontrain.cc
@@ -143,7 +143,7 @@ int Smooth::geoCutOff(const vector &lencount, vector& result){
     Double relDiff;
 
     /*
-     * start with dtemp as the positiion of the maximum of the length distribution
+     * start with dtemp as the position of the maximum of the length distribution
      * increase dtemp and check the size of the jump of the model-distribution
      * if we introduce the cutoff at dtemp
      */
diff --git a/src/compgenepred.cc b/src/compgenepred.cc
index b1bc78b9..2490ab16 100644
--- a/src/compgenepred.cc
+++ b/src/compgenepred.cc
@@ -530,7 +530,7 @@ void CompGenePred::start(){
        
 	if(use_omega){
 	    geneRange->computeOmegasEff(hects, seqRanges, &ctree, &codonAli); // omega and number of substitutions is stored as OrthoExon attribute
-	    // calculates an omega for every single codon alignment and prints wiggle trac for ever reding frame and species combination that exists in an ortho exon
+	    // calculates an omega for every single codon alignment and prints wiggle trac for ever reading frame and species combination that exists in an ortho exon
 	    //geneRange->printOmegaForCodon(outdir);
 	    //inefficient omega calculation, only use for debugging purpose 
 	    //geneRange->computeOmegas(hects, seqRanges, &ctree);
@@ -593,7 +593,7 @@ void CompGenePred::start(){
     GeneMSA::topologies.clear(); 
   
     if(Properties::hasProperty("referenceFile")){
-      // initialise training of log reg parameters
+      // initialize training of log reg parameters
       train_OEscore_params(speciesNames.size());
     }
   } 
diff --git a/src/consensus.cc b/src/consensus.cc
index 12ad5666..05ac5cac 100644
--- a/src/consensus.cc
+++ b/src/consensus.cc
@@ -13,7 +13,7 @@ const int nRep=20;
 using namespace std;
 
 consensus::consensus(int starting1,int ending1){
-  //gives default value to the paramters
+  //gives default value to the parameters
   pattern_size=6;
   p_value=.01;
   delta=2;
@@ -41,7 +41,7 @@ consensus::consensus(int starting1,int ending1){
   for(i=pattern_size-1;i>=0;i--) 
     powers.push_back(pow((double)4,(double)i));
 
-  //initialises the mean value, significance value, relevant value vectors
+  //initializes the mean value, significance value, relevant value vectors
   for(i=0;iprev_neighbours[i])
 	  prev_neighbours[j]=prev_neighbours[j]-1;
@@ -470,7 +470,7 @@ void consensus::start(){
   for(k=0;kmax_freq)
-	      max_freq=final_list[k].position_of_occurence[j];
+	    final_list[k].position_of_occurrence[j]++;
+	    if(final_list[k].position_of_occurrence[j]>max_freq)
+	      max_freq=final_list[k].position_of_occurrence[j];
 	  }
 	}
 	catch(exception& e ){
@@ -533,7 +533,7 @@ void consensus::analyse(string pattern1,float p_value1,float delta1,int max_allo
 	tpm[row][column]++;
     }
   }
-  //calculating the background probabilites
+  //calculating the background probabilities
   float k1=0;
   for(i=0;i<4;i++){
     k1=0;
@@ -572,7 +572,7 @@ void consensus::analyse(string pattern1,float p_value1,float delta1,int max_allo
     }
   }
 
-  cout << " calculated the frequenecy values" << endl;
+  cout << " calculated the frequency values" << endl;
   data1.consensus_pattern=analyse_pattern;
   data1.f_value=f_values[number];
 
@@ -619,16 +619,16 @@ void consensus::analyse(string pattern1,float p_value1,float delta1,int max_allo
   for(k=0;kmax_freq)
-	      max_freq=final_list[k].position_of_occurence[j];
+	    final_list[k].position_of_occurrence[j]++;
+	    if(final_list[k].position_of_occurrence[j]>max_freq)
+	      max_freq=final_list[k].position_of_occurrence[j];
 	  }
 	}
 	catch(exception& e ){
@@ -644,18 +644,18 @@ void consensus::plot_histogram(){
   for(i=0;i1)     probability of omega > 1 at alipos (*: Pr(w>1) > 0.90, **: Pr(w>1) > 0.95)\n";
   cout << "# 5. post_mean   posterior mean estimate of omega at ali_pos\n";
   cout << "# 6. SE_for_w    standard deviation of omega at ali_pos\n";
-  cout << "# 7. num_subst   number of subsitution calculated by the Fitch algorithm\n\n";
+  cout << "# 7. num_subst   number of substitution calculated by the Fitch algorithm\n\n";
 }
diff --git a/src/evaluation.cc b/src/evaluation.cc
index 19d35bda..7f8156e9 100644
--- a/src/evaluation.cc
+++ b/src/evaluation.cc
@@ -127,7 +127,7 @@ void Evaluation::addToEvaluation(Transcript* predictedGeneList, Transcript* anno
     numUniquePredExons += predictedExons->size();
 
 
-    // evaluateQuickOnNukleotideLevel(predictedExons.first, -1, annotatedExons.first, -1);
+    // evaluateQuickOnNucleotideLevel(predictedExons.first, -1, annotatedExons.first, -1);
     evaluateOnNucleotideLevel(predictedExons, annotatedExons); // coding bases only
     evaluateOnExonLevel(predictedExons, annotatedExons);
     evaluateOnGeneLevel(predictedGeneList, annotatedGeneList);
diff --git a/src/exon_seg.cc b/src/exon_seg.cc
index 05e4b690..d914509d 100644
--- a/src/exon_seg.cc
+++ b/src/exon_seg.cc
@@ -17,7 +17,7 @@
 using namespace std;
 
   exon_segmentation::exon_segmentation(){
-    /* Initialise lambda1 and lambda2
+    /* Initialize lambda1 and lambda2
      */
     lambda1=0.2;
     lambda2=0.3;
@@ -71,13 +71,13 @@ using namespace std;
 
 
 
-    /* Initialise the values of lambda1 and lambda2 in the order of
+    /* Initialize the values of lambda1 and lambda2 in the order of
      * 1/(mean coverage depth)
      */
     /*lambda2=(1/coverage_info.avg_depth)*1.1;
     lambda1=(1/coverage_info.avg_depth)*0.9;
 
-     Initialise the p1 and p2 vectors
+     Initialize the p1 and p2 vectors
      */
     //p1.resize(maxcov+1,0.0);
     //p2.resize(maxcov+1,0.0);
@@ -167,26 +167,26 @@ using namespace std;
   void exon_segmentation::train_function(dataset &coverage_info,string inputfile,string key){
     int find1,i,start=0,end=0,seg_ptr,track,strand,l,depth;
     double sum_exons=0,sum_introns=0,sum_q_exon_num=0,sum_q_exon_den=0,sum_q_intron_num=0,sum_q_intron_den=0;
-    /* r stores the fraction of postitions with coverage depths > L
+    /* r stores the fraction of positions with coverage depths > L
      * q is a parameter such that L+1/q= "mean of coverages that are >L "
      * log_comp_q stores the value of log(1-q) for introns and exons
      */
     double q_intron,q_exon,log_comp_q_intron,log_comp_q_exon,r_exon=0,r_intron=0;
     ifstream infile(inputfile.c_str());
     string fileline,feature,strand1,line;
-    /* stores the number of positions with a parrticular coverage depth
+    /* stores the number of positions with a particular coverage depth
      */
     vector count_introns,count_exons;
     /* stores the normalized value of the count vector
      */
     vector f_introns,f_exons,temp1;
-    /*structure where the data inormation from the training gff file is stored
+    /*structure where the data information from the training gff file is stored
      */
     vector segments;
     /* a temporary fragment is defined to store the data initially and then it is pushed to the vector
      */
     fragment temp;
-    /* initialise the vectors
+    /* initialize the vectors
      */
     count_introns.resize(maxcov+1,0);
     count_exons.resize(maxcov+1,0);
@@ -196,7 +196,7 @@ using namespace std;
     prob_dist_exon.resize(coverage_info.no_of_tracks,temp1);
     prob_dist_intron.resize(coverage_info.no_of_tracks,temp1);
 
-    /* We read the input gff file and store the information about introns and exons in a vector os fragments
+    /* We read the input gff file and store the information about introns and exons in a vector of fragments
      */
     getline(infile,line);
     while(!infile.eof() ){
@@ -216,7 +216,7 @@ using namespace std;
 	/* loops through the number of tabs possible in a line
 	 */
 	for(i=0;i<8;i++){
-	  /* extract the relevant information from the corrsponding i
+	  /* extract the relevant information from the corresponding i
 	   */
 	  if(i==2)
 	    feature=fileline.substr(0,find1);
@@ -306,7 +306,7 @@ using namespace std;
       }
       q_exon=sum_q_exon_den/sum_q_exon_num;
       q_intron=sum_q_intron_den/sum_q_intron_num;
-      /* initialise the probability distribution vectors
+      /* initialize the probability distribution vectors
        */
       log_comp_q_intron=log(1-q_intron);
       log_comp_q_exon=log(1-q_exon);
@@ -388,7 +388,7 @@ using namespace std;
      * first track of the + strand only
      */
     for(l=0;l > &emission_probs,int max_len,vector< vector< vector > > &input_set,int chunksize,int iteration){
   int i,j,m,index,strand,track,limit;
-    /* g_matrix is used to store the probaility values temporarily so as to
+    /* g_matrix is used to store the probability values temporarily so as to
      * reduce the time complexity in states having length > 1
      */
     vector > g_matrix;
-    /*define temporary vectors to initialise higher dimension vectors
+    /*define temporary vectors to initialize higher dimension vectors
      */
     vector temp,temp1;
     double sum,sum1;
@@ -673,7 +673,7 @@ void exon_segmentation::calculate_emissions( vector< vector > &emission_
 	g_matrix.push_back(temp);
     }
     /* Calculate the size of the current chunk and store it in limit so as to 
-     * avoid index overflow in tha dataset
+     * avoid index overflow in the dataset
      */
     if((iteration+1)*chunksize >max_len)
       limit=max_len-iteration*chunksize;
@@ -704,8 +704,8 @@ void exon_segmentation::calculate_emissions( vector< vector > &emission_
 		 * here we also add the offset determined by the chunksize and the number of iteration
 		 */
 		index=input_set[strand][track][j+1-m+iteration*chunksize];
-		/* if the strand amd the label are compatiable then use the
-		 * probabiliity distribution for exons
+		/* if the strand and the label are compatible then use the
+		 * probability distribution for exons
 		 */
 		if( (i==EXONP && (strand!=STRANDM))||(i==EXONM && (strand!=STRANDP)) ){
 		  sum=sum+prob_value_exon(index,track);
@@ -727,13 +727,13 @@ void exon_segmentation::calculate_emissions( vector< vector > &emission_
 	/* for the states with length > 1 we use the previously calculated g values to find the emission probability
 	 */
 	else{
-	  sum=0;//initialise the value of sum
+	  sum=0;//initialize the value of sum
 	  /* first we calculate the next g value
 	   */
 	  for(strand=0;strand<3;strand++){
 	    for(track=0;track > &emission_
 		sum=sum+prob_value_intron(index,track);	    	    
 	    }
 	    g_matrix[i][j]=sum;//stores the value of g
-	    /* calculates emission value by adding the head value and substracting 
+	    /* calculates emission value by adding the head value and subtracting 
 	     * the tail value to the previous entry in g_matrix
 	     */
 	    emission_probs[i][j]=emission_probs[i][j-1]+g_matrix[i][j]-g_matrix[i][j-lengths[i]];
@@ -765,7 +765,7 @@ void exon_segmentation::calculate_emissions( vector< vector > &emission_
     /* else we take the maximum through all possible states k
      */
     else{
-      max=minus_infinity;//initialise max
+      max=minus_infinity;//initialize max
       for(k=0;k exon_segmentation::viterbi(vector< vector< vector > > &input_se
     else
       limit=chunksize;
     
-    /* initialise the dynamic programming matrix
+    /* initialize the dynamic programming matrix
      */
     temp.clear();//clears the temporary vectors
     for(i=0;i exon_segmentation::viterbi(vector< vector< vector > > &input_se
     }
     gamma.resize(limit+1,temp);
     
-    /* initialise the emission probability matrix
+    /* initialize the emission probability matrix
      */
     temp.clear();
     temp.resize(limit,0.0);
@@ -833,7 +833,7 @@ vector exon_segmentation::viterbi(vector< vector< vector > > &input_se
     cout<<"tesint "< exon_segmentation::viterbi(vector< vector< vector > > &input_se
 	fill_viterbi(gamma,NUMSTATES,j,s,sum1,a,&spred);
       }
 
-    /* bactracking to get the sequence
+    /* backtracking to get the sequence
      */
     j=limit;
     max=minus_infinity;
@@ -889,7 +889,7 @@ vector exon_segmentation::viterbi(vector< vector< vector > > &input_se
       else{
 	/* once we reach a different state we store the stretch of information
 	 */
-	/* Initialise the vector to store the average coverage depth
+	/* Initialize the vector to store the average coverage depth
 	 * for each experiment
 	 */
 	temp1.resize(no_of_tracks,0.0);
@@ -975,7 +975,7 @@ vector exon_segmentation::viterbi(vector< vector< vector > > &input_se
 
   }
 /* Function to convert the average coverage depths into some usable form
- * in teh pott's functional
+ * in the pott's functional
  */
 double exon_segmentation::pott_convert(double d){
   if(d<1)
@@ -1014,7 +1014,7 @@ double exon_segmentation::pott_convert(double d){
      * psum stores the summation of l_i*c_i
      * psqrsum stores the summation l_i*c_i^2
      * pcubesum stores the summation l_i*c_i^3
-     * psuml stores the summattion l_i
+     * psuml stores the summation l_i
      */
     temp2.resize(n+1,0.0);
     psum.resize(no_of_tracks,temp2);
@@ -1022,7 +1022,7 @@ double exon_segmentation::pott_convert(double d){
     pcubesum.resize(no_of_tracks,temp2);
     psum1.resize(no_of_tracks,temp1);
 
-    /* initialize the vectors required for the dynamic programing matrix
+    /* initialize the vectors required for the dynamic programming matrix
      */
     h.resize(n+1,0.0);
     x.resize(no_of_tracks,temp2);
@@ -1046,19 +1046,19 @@ double exon_segmentation::pott_convert(double d){
       }
     }
     k=0;
-    /* Intialiazation for the first element of the dynamic programing table
+    /* Initialization for the first element of the dynamic programming table
      */
     /* Change the value of pott_gamma to no_of_tracks*pott_gamma
      * to account for multiple number of experiments in the file
      */
     h[0]=-1*pott_gamma*no_of_tracks;
-    /* Start the dynamic programing algorithm
+    /* Start the dynamic programming algorithm
      */
     for(k=1;k<=n;k++){
       /* Initialize min value to the first entry
        */
       sum=0;
-      /* sum the calue of s over all the experimetns
+      /* sum the value of s over all the experiments
        */
       for(exp=0;expfirst<
 
 /*
- * Initialisation of static data members
+ * Initialization of static data members
  */
 
 vector ExonModel::patterncount[3];      // {0,1,2}x{acgt}^(k+1), the reading frame is 
-                                                 // the positiion of the emitted (last) nucleotide
+                                                 // the position of the emitted (last) nucleotide
 vector ExonModel::initpatterncount[3];
 vector ExonModel::etpatterncount[3];
 Integer ExonModel::k = 4;
@@ -64,7 +64,7 @@ Boolean ExonModel::hasLenDist = false;
 //Boolean ExonModel::hasAAdep = false;      // not in use right now
 Integer ExonModel::gesbasen[3]  = { 0, 0, 0 };
 Double  ExonModel::patpseudo = 1;         // pseudocount for patterns in sequence
-Integer ExonModel::exonLenD = 4000;       // use detailled length distribution up to this number
+Integer ExonModel::exonLenD = 4000;       // use detailed length distribution up to this number
 Integer ExonModel::minPatSum = 0;         // for the decision to shorten the emission pattern
 vector ExonModel::lenCountSingle;   // length count of Single exons (length of biol. exon)
 vector ExonModel::lenCountInitial;  // length count of Initial exons (length of biol. exon)
@@ -280,13 +280,13 @@ int ExonModel::getInnerPartEndOffset(StateType type){
  * destructor
  */
 ExonModel::~ExonModel( ){
-    // TODO: delete what is neccessary
+    // TODO: delete what is necessary
     if( --exoncount == 0 )
 	lastParIndex = -1;
 }
 
 /*
- * ===[ ExonModel initialisation of class variables ]======================
+ * ===[ ExonModel initialization of class variables ]======================
  */
 void ExonModel::init() {
     /*
@@ -1003,7 +1003,7 @@ void ExonModel::viterbiForwardAndSampling(ViterbiMatrixType& viterbi, // matrix
 		     << endl;
 #endif
 #endif		    
-	    // if it's a terminal or rinitial exon, we backtrack from igenic which is
+	    // if it's a terminal or initial exon, we backtrack from igenic which is
 	    // unaware of substates, so the given state won't refer to a substate; 
 	    // in order to find out, we check viterbi: if the probability comes from the
 	    // profile, there will be substates, otherwise not
@@ -1403,7 +1403,7 @@ Double ExonModel::endPartEmiProb(int end) const {
 /*
  * ===[ ExonModel::notEndPartEmiProb ]=====================================
  *
- * Probability of the emission of the exon exluding the fixed length end part.
+ * Probability of the emission of the exon excluding the fixed length end part.
  * This includes 
  * - the beginPart     (translation initiation, ass or reverse dss)
  * - the startSeq part (first k or less emissions after the begin part)
@@ -1581,7 +1581,7 @@ Double ExonModel::notEndPartEmiProb(int beginOfStart, int right, int frameOfRigh
 	 * inner sequence part from endOfStart+1 to right
 	 * | initial pattern | initial content model| exon content model| exon terminating model (dss)|
 	 * Depending on the exon type, some of the models may not apply
-	 * For short exons the precedence is inital -> terminal -> inner
+	 * For short exons the precedence is initial -> terminal -> inner
 	 * but terminal applies only completely or not at all.
 	 */
 	int endOfInitial, beginOfTerm,  endOfStart; // forward
@@ -1929,7 +1929,7 @@ Double ExonModel::seqProb(int left, int right, int frameOfRight) const {
 
     bool reverse = !isOnFStrand(etype);
     Seq2Int s2i(k+1);
-    if (left < 0) {   // new initialisation
+    if (left < 0) {   // new initialization
 	seqProb = 1;
         oldleft = oldright = oldframe = -1;
         oldtype = TYPE_UNKNOWN;
diff --git a/src/extrinsicinfo.cc b/src/extrinsicinfo.cc
index cbfbdbbd..2a2839d1 100644
--- a/src/extrinsicinfo.cc
+++ b/src/extrinsicinfo.cc
@@ -907,7 +907,7 @@ Feature *SequenceFeatureCollection::getExonListOvlpingRange(int startPosition, i
 
 /*
  * makeGroups
- * makes groups of hints accoding to the group name given in the hintsfile
+ * makes groups of hints according to the group name given in the hintsfile
  */ 
 void SequenceFeatureCollection::makeGroups(){
     // HashTable, 100000 > groupnames;
@@ -1339,7 +1339,7 @@ list::iterator SequenceFeatureCollection::getPosStartAfter(int type, in
 
 /*
  * rescaleBoniByConformance
- * Adjust boni of all hints, accoding to the number of other hints that are supporting it and the number 
+ * Adjust boni of all hints, according to the number of other hints that are supporting it and the number 
  * of other hints that are contradicting it.
  * A hint with a lot of contradicting other hints gets a smaller bonus.
  */
@@ -2406,8 +2406,8 @@ int FeatureCollection::getNumCommonSeqs(AnnoSequence *annoseq){
 void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence* annoseqs, bool cleanRedundancies){
 /*
  * Loop over all genes in the set and count for each feature
- * the relative frequency of its occurence at positions where it is correct
- * and the relative frequency of its occurence at positions where it is not correct
+ * the relative frequency of its occurrence at positions where it is correct
+ * and the relative frequency of its occurrence at positions where it is not correct
  */
 
     int num_correct[NUM_FEATURE_TYPES];
@@ -2860,6 +2860,6 @@ void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence* annoseqs
 
 
 /*
- * TODO: clean for redundancies after cheking the accuracy. Then delete the less confident type.
+ * TODO: clean for redundancies after checking the accuracy. Then delete the less confident type.
  * Check the configuration file syntax. E.g. when the number of grades is missing.
  */
diff --git a/src/gene.cc b/src/gene.cc
index 100a07c7..6364eb89 100644
--- a/src/gene.cc
+++ b/src/gene.cc
@@ -1672,7 +1672,7 @@ void Gene::compileExtrinsicEvidence(list  *groupList){
 	    sf = supportingFraction(&*git);
 	    if (sf >= 1.0) {
 		supportingEvidence->add(git->getSource(), git->getName());
-	    } else { // TODO: in case of CDS only predictions the rest does not need to be incompatible neccessarily
+	    } else { // TODO: in case of CDS only predictions the rest does not need to be incompatible necessarily
 		incompatibleEvidence->add(git->getSource(), git->getName());
 	    }
 	    addSupportedStates(&*git);
diff --git a/src/hints.cc b/src/hints.cc
index f763c4ca..ba1ca380 100644
--- a/src/hints.cc
+++ b/src/hints.cc
@@ -290,8 +290,8 @@ FeatureType Feature::getFeatureType(int typeint){
  */
 bool Feature::compatibleWith(Feature &other){
     const int transcript_fuzzy_margin = 50; // a tss/tts at most this far from the end of an exon/UTR end is still considered compatible
-    const int term3_M = 1000; // two tts at most this far apart but not overlapping and not suggesting tail to tail genes are imcompatible
-    const int term5_M = 0; // two tss at most this far apart but not overlapping and not suggesting head to head genes are imcompatible
+    const int term3_M = 1000; // two tts at most this far apart but not overlapping and not suggesting tail to tail genes are incompatible
+    const int term5_M = 0; // two tss at most this far apart but not overlapping and not suggesting head to head genes are incompatible
     
     if (start > other.end || end < other.start){ // no overlap
 	if ((type == tssF && other.type == tssF) &&
@@ -445,7 +445,7 @@ bool Feature::compatibleWith(Feature &other){
  * Feature::weakerThan
  * True if every gene structure that is compatible with 'other' also is compatible with 'this'.
  * Strictly is true, if there could be gene structures that are only compatible with 'this' and not with other.
- * Usually, when a **partF inverval is larger in other. 'strictly' is only correctly set when the return value is true.
+ * Usually, when a **partF interval is larger in other. 'strictly' is only correctly set when the return value is true.
  */
 bool Feature::weakerThan(Feature &other, bool &strictly){
     strictly = false;
@@ -585,7 +585,7 @@ void HintGroup::addFeature(Feature *hint){
     while(fit != hints->end() && (*fit)->end < hint->end)
 	fit++;
     hints->insert(fit, hint);
-    // if feature is genic then reset begin and end if neccessary
+    // if feature is genic then reset begin and end if necessary
     // nongenic features: irpartF, nonexonpartF
     if (begin < 0 || begin > hint->start)
 	begin = hint->start;
diff --git a/src/igenicmodel.cc b/src/igenicmodel.cc
index bb2f0a74..bb7020a5 100644
--- a/src/igenicmodel.cc
+++ b/src/igenicmodel.cc
@@ -21,7 +21,7 @@
 #include 
 
 /*
- * Initialisation of static data members
+ * Initialization of static data members
  */
 
 Integer IGenicModel::k = 4;
@@ -38,7 +38,7 @@ int IGenicModel::verbosity;
 double IGenicModel::geoProb = 0.9999;
 
 /*
- * Initialisation of class variables
+ * Initialization of class variables
  */
 void IGenicModel::init() {
     try{
diff --git a/src/intronmodel.cc b/src/intronmodel.cc
index 86c6b8f7..b4a17356 100644
--- a/src/intronmodel.cc
+++ b/src/intronmodel.cc
@@ -19,7 +19,7 @@
 #include 
 
 /*
- * Initialisation of static data members
+ * Initialization of static data members
  */
 vector IntronModel::emicount;
 vector IntronModel::intlencount;
@@ -99,7 +99,7 @@ IntronModel::~IntronModel( ){
 }
 
 /*
- * IntronModel initialisation of class variables
+ * IntronModel initialization of class variables
  */
 void IntronModel::init() {
     // Initialize class variables from properties values
@@ -1041,7 +1041,7 @@ Double IntronModel::seqProb(int left, int right) const {
     
     int curpos;
     Seq2Int s2i(k+1);
-    if (left < 0) {   // new initialisation
+    if (left < 0) {   // new initialization
 	seqProb = 1;
 	oldleft = oldright = -1;
 	seqProbs.assign(d - DSS_MIDDLE - Constant::dss_end - Constant::ass_start 
diff --git a/src/load2sqlitedb.cc b/src/load2sqlitedb.cc
index 9b66caf8..b66b1d1e 100644
--- a/src/load2sqlitedb.cc
+++ b/src/load2sqlitedb.cc
@@ -370,12 +370,12 @@ parameters:\n\
 --noIdx       use this flag to suppress the building of indices on the database tables.\n\
               If you are going to load several genomes and/or hint files in a row, this option\n\
               is recommended to speed up the loading. But make sure to build indices with\n\
-              --makeIdx after all genomes/hints are loaded. Otherwise, data retrieval opterations\n\
+              --makeIdx after all genomes/hints are loaded. Otherwise, data retrieval operations\n\
               can be very slow.\n\
 --makeIdx     use this flag to build the indices on the database tables after loading several\n\
               genomes and/or hint files with --noIdx. Only call this once for all species, e.g.\n\
               load2sqlitedb --makeIdx --dbaccess=database.db\n\
---clean       makes a clean load deleting existing hints/genome for the species from the dabase.\n\
+--clean       makes a clean load deleting existing hints/genome for the species from the database.\n\
               When called with a gff file, only the hints for the species are delete, but not the genome.\n\
               When called with a fasta file, both hints and genome for the species are deleted.\n\
 \n\
diff --git a/src/motif.cc b/src/motif.cc
index a472fb03..1f9153af 100644
--- a/src/motif.cc
+++ b/src/motif.cc
@@ -94,7 +94,7 @@ void BaseCount::addCharacter(char nucleotide, bool subtract){
 // 	case 2: return rg;
 // 	case 3: return rt;
 // 	default: 
-// 	    throw InvalidNukleotideError("");
+// 	    throw InvalidNucleotideError("");
 //     }
 // }
 
diff --git a/src/namgene.cc b/src/namgene.cc
index a8546fc2..49353c93 100644
--- a/src/namgene.cc
+++ b/src/namgene.cc
@@ -899,7 +899,7 @@ list *NAMGene::findGenes(const char *dna, Strand strand, bool onlyViter
 	    (*geneit1)->updatePostProb(*geneit2);
     }
     for (geneit1 = alltranscripts.begin(); geneit1 != alltranscripts.end(); geneit1++){
-	(*geneit1)->normPostProb(sampleiterations); // +1 wegen Viterbipfad
+	(*geneit1)->normPostProb(sampleiterations); // +1 due to  Viterbi path
     }
   }
   /*
@@ -931,7 +931,7 @@ list *NAMGene::findGenes(const char *dna, Strand strand, bool onlyViter
   if (sampleiterations>1) {
     /*
      * compute apostprob of genes. The posterior 'probability' of a gene is the 
-     * expected number of transcripts overlaping the region of the gene on 
+     * expected number of transcripts overlapping the region of the gene on 
      * the given strand. This may now be larger than 1 (changed March 15, Mario).
      */
     for (agit = agl->begin(); agit != agl->end(); ++agit) {
@@ -1053,7 +1053,7 @@ int NAMGene::getNextCutEndPoint(const char *dna, int beginPos, int maxstep, Sequ
       StateModel::setSFC(partSFC);
       viterbiAndForward(curdna);      // do not use protein profile here
       viterbiPath = getViterbiPath(curdna, "temp");
-      delete partSFC; //achtung, das muß nach getViterbiPath stehen
+      delete partSFC; //attention, this should called after getViterbiPath
       delete [] curdna;
       condensedViterbiPath = StatePath::condenseStatePath(viterbiPath);
       //cout << "getNextCutEndPoint viterbi path:" << endl;
diff --git a/src/ncmodel.cc b/src/ncmodel.cc
index 3b49f40d..a826f999 100644
--- a/src/ncmodel.cc
+++ b/src/ncmodel.cc
@@ -20,7 +20,7 @@
 #include 
 
 /*
- * Initialisation of static data members
+ * Initialization of static data members
  */
 Integer         NcModel::nccount = 0;
 vector  NcModel::lenDistInternal;     // length distribution of non-single exons
@@ -54,7 +54,7 @@ NcModel::~NcModel( ){
 }
 
 /*
- * NcModel initialisation of class variables
+ * NcModel initialization of class variables
  */
 void NcModel::init() {
     try {
diff --git a/src/properties.cc b/src/properties.cc
index 03a1ab84..b95433c4 100644
--- a/src/properties.cc
+++ b/src/properties.cc
@@ -412,7 +412,7 @@ void Properties::init( int argc, char* argv[] ){
 	}
     }
     if (configPath[configPath.size()-1] != '/')
-	configPath += '/';  // append slash if neccessary
+	configPath += '/';  // append slash if necessary
 
     // does the directory actually exist?
     struct stat buffer;
diff --git a/src/utrmodel.cc b/src/utrmodel.cc
index 1fd09c1e..55262fac 100644
--- a/src/utrmodel.cc
+++ b/src/utrmodel.cc
@@ -18,7 +18,7 @@
 #include 
 
 /*
- * Initialisation of static data members
+ * Initialization of static data members
  */
 Integer         UtrModel::utrcount = 0;
 vector UtrModel::utr5_emicount;
@@ -853,7 +853,7 @@ void UtrModel::viterbiForwardAndSampling( ViterbiMatrixType& viterbi,
 	    leftMostEndOfPred = base - (max_exon_length - Constant::trans_init_window + Constant::ass_upwindow_size + Constant::ass_start + ASS_MIDDLE);
 	    rightMostEndOfPred = base - Constant::ass_upwindow_size - Constant::ass_whole_size();
 	    if (- Constant::ass_upwindow_size - Constant::ass_whole_size() + Constant::trans_init_window + Constant::ass_end < 0) 
-		// this check is neccessary, otherwise endOfPred could be larger than base
+		// this check is necessary, otherwise endOfPred could be larger than base
 		rightMostEndOfPred = base - Constant::ass_upwindow_size - Constant::ass_whole_size()
 		    + Constant::trans_init_window + Constant::ass_end; // this is so 5' terminal exons can be shorter than trans_init_window + ass_end, negative length of state!
 	                                                               // in the most extreme case, the UTR exon has length 0
@@ -862,7 +862,7 @@ void UtrModel::viterbiForwardAndSampling( ViterbiMatrixType& viterbi,
 	    leftMostEndOfPred = base - (max_exon_length - Constant::trans_init_window + Constant::ass_upwindow_size + Constant::ass_start + ASS_MIDDLE);
 	    rightMostEndOfPred = base - Constant::ass_upwindow_size - Constant::ass_whole_size();
 	    if (- Constant::ass_upwindow_size - Constant::ass_whole_size() + Constant::trans_init_window + Constant::ass_end < 0) 
-		// this check is neccessary, otherwise endOfPred could be larger than base
+		// this check is necessary, otherwise endOfPred could be larger than base
 		rightMostEndOfPred = base - Constant::ass_upwindow_size - Constant::ass_whole_size()
 		    + Constant::trans_init_window + Constant::ass_end; // this is so 5' terminal exons can be shorter than trans_init_window, negative length of state!
 	    break;
diff --git a/src/utrtrain.cc b/src/utrtrain.cc
index 3e64b9ee..1a25cc73 100644
--- a/src/utrtrain.cc
+++ b/src/utrtrain.cc
@@ -140,7 +140,7 @@ void UtrModel::buildProbabilities(const AnnoSequence* annoseq){
     utr5_emiprobs.order = k;
     computeEmiFromPat(patternprobs, utr5_emiprobs.probs, k);    
 
-    // 5' utr initial emission (inital exon and single exon)
+    // 5' utr initial emission (initial exon and single exon)
     patternprobs.resize(utr5init_emicount.size());
     makeProbsFromCounts(patternprobs, utr5init_emicount, k, utr_patpseudo, false);
     utr5init_emiprobs.probs.resize(utr5init_emicount.size());