From aee62aec470236523bcc08d834a79f25912bdf70 Mon Sep 17 00:00:00 2001 From: hmehlan Date: Wed, 7 Nov 2018 11:57:31 +0100 Subject: [PATCH] fix typo recomment -> recommend --- .../Conidiobolus_coronatus_parameters.cfg | 2 +- config/species/E_coli_K12/E_coli_K12_parameters.cfg | 2 +- .../Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg | 2 +- config/species/adorsata/adorsata_parameters.cfg | 2 +- .../ancylostoma_ceylanicum_parameters.cfg | 2 +- config/species/b_pseudomallei/b_pseudomallei_parameters.cfg | 2 +- .../species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1 | 2 +- .../species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2 | 2 +- .../species/bombus_impatiens1/bombus_impatiens1_parameters.cfg | 2 +- .../bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1 | 2 +- .../bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2 | 2 +- .../bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3 | 2 +- .../bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4 | 2 +- .../bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5 | 2 +- .../bombus_terrestris2/bombus_terrestris2_parameters.cfg | 2 +- .../bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1 | 2 +- .../bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2 | 2 +- .../bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3 | 2 +- .../bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4 | 2 +- config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg | 2 +- config/species/cacao/cacao_parameters.cfg | 2 +- config/species/caenorhabditis/caenorhabditis_parameters.cfg | 2 +- .../camponotus_floridanus/camponotus_floridanus_parameters.cfg | 2 +- config/species/chicken/chicken_parameters.cfg | 2 +- config/species/chiloscyllium/chiloscyllium_parameters.cfg | 2 +- config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1 | 2 +- config/species/ciona/ciona_parameters.cfg | 2 +- config/species/ciona/ciona_parameters.cfg.orig1 | 2 +- config/species/coyote_tobacco/coyote_tobacco_parameters.cfg | 2 +- config/species/elephant_shark/elephant_shark_parameters.cfg | 2 +- config/species/fly/fly_parameters.cfg | 2 +- config/species/fly_exp/fly_exp_parameters.cfg | 2 +- config/species/generic/generic_parameters.cfg | 2 +- .../heliconius_melpomene1/heliconius_melpomene1_parameters.cfg | 2 +- config/species/honeybee1/honeybee1_parameters.cfg | 2 +- config/species/honeybee1/honeybee1_parameters.cfg.orig1 | 2 +- config/species/japaneselamprey/japaneselamprey_parameters.cfg | 2 +- .../leishmania_tarentolae/leishmania_tarentolae_parameters.cfg | 2 +- config/species/maize/maize_parameters.cfg | 2 +- config/species/maize5/maize5_parameters.cfg | 2 +- .../species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg | 2 +- .../nematostella_vectensis_parameters.cfg | 2 +- config/species/parasteatoda/parasteatoda_parameters.cfg | 2 +- config/species/pfalciparum/pfalciparum_parameters.cfg | 2 +- config/species/pisaster/pisaster_parameters.cfg | 2 +- config/species/rhincodon/rhincodon_parameters.cfg | 2 +- config/species/rhincodon/rhincodon_parameters.cfg.orig1 | 2 +- config/species/rhodnius/rhodnius_parameters.cfg | 2 +- config/species/rice/rice_parameters.cfg | 2 +- config/species/s_aureus/s_aureus_parameters.cfg | 2 +- config/species/s_pneumoniae/s_pneumoniae_parameters.cfg | 2 +- config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1 | 2 +- config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2 | 2 +- config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3 | 2 +- config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4 | 2 +- config/species/schistosoma2/schistosoma2_parameters.cfg | 2 +- config/species/scyliorhinus/scyliorhinus_parameters.cfg | 2 +- config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1 | 2 +- .../strongylocentrotus_purpuratus_parameters.cfg | 2 +- .../sulfolobus_solfataricus_parameters.cfg | 2 +- .../template_prokaryotic/template_prokaryotic_parameters.cfg | 2 +- .../thermoanaerobacter_tengcongensis_parameters.cfg | 2 +- config/species/tomato/tomato_parameters.cfg | 2 +- config/species/toxoplasma/toxoplasma_parameters.cfg | 2 +- config/species/trichinella/trichinella_parameters.cfg | 2 +- .../verticillium_albo_atrum1_parameters.cfg | 2 +- .../verticillium_longisporum1_parameters.cfg | 2 +- .../verticillium_longisporum1_parameters.cfg.orig1 | 2 +- config/species/volvox/volvox_parameters.cfg | 2 +- config/species/wheat/wheat_parameters.cfg | 2 +- config/species/zebrafish/zebrafish_parameters.cfg | 2 +- 71 files changed, 71 insertions(+), 71 deletions(-) diff --git a/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg b/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg index 8ea11d9c..3755f672 100644 --- a/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg +++ b/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg @@ -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 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 f0151ed3..394312b1 100644 --- a/config/species/E_coli_K12/E_coli_K12_parameters.cfg +++ b/config/species/E_coli_K12/E_coli_K12_parameters.cfg @@ -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 diff --git a/config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg b/config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg index e392d1a3..ca994edf 100644 --- a/config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg +++ b/config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg @@ -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 diff --git a/config/species/adorsata/adorsata_parameters.cfg b/config/species/adorsata/adorsata_parameters.cfg index c2a1c605..cb442970 100644 --- a/config/species/adorsata/adorsata_parameters.cfg +++ b/config/species/adorsata/adorsata_parameters.cfg @@ -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 diff --git a/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg b/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg index feff42c3..f38118a2 100644 --- a/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg +++ b/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg @@ -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 diff --git a/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg b/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg index 5d6eec75..f68a6c3e 100644 --- a/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg +++ b/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg @@ -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 diff --git a/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1 b/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1 index dd64aae5..ad8cf4f4 100644 --- a/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1 +++ b/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1 @@ -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 diff --git a/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2 b/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2 index dd64aae5..ad8cf4f4 100644 --- a/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2 +++ b/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2 @@ -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 diff --git a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg index 4291e687..13048ce4 100644 --- a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg +++ b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg @@ -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 diff --git a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1 b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1 index be27cba2..57ba868a 100644 --- a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1 +++ b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1 @@ -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 diff --git a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2 b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2 index 870e9aed..3500620a 100644 --- a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2 +++ b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2 @@ -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 diff --git a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3 b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3 index 0c3940a9..154cb452 100644 --- a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3 +++ b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3 @@ -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 diff --git a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4 b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4 index 66b25a2c..8890fa70 100644 --- a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4 +++ b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4 @@ -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 diff --git a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5 b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5 index bf178276..d91a3a9a 100644 --- a/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5 +++ b/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5 @@ -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 diff --git a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg index ad6e3858..ee27a769 100644 --- a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg +++ b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg @@ -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 diff --git a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1 b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1 index bdcec349..35c40650 100644 --- a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1 +++ b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1 @@ -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 diff --git a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2 b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2 index 68433dd4..ac5a82b9 100644 --- a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2 +++ b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2 @@ -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 diff --git a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3 b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3 index 38f31cac..34776fd6 100644 --- a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3 +++ b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3 @@ -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 diff --git a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4 b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4 index 38f31cac..34776fd6 100644 --- a/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4 +++ b/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4 @@ -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 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 21124c49..54e94eeb 100644 --- a/config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg +++ b/config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg @@ -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 diff --git a/config/species/cacao/cacao_parameters.cfg b/config/species/cacao/cacao_parameters.cfg index 8b35b653..1f9d8999 100644 --- a/config/species/cacao/cacao_parameters.cfg +++ b/config/species/cacao/cacao_parameters.cfg @@ -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 diff --git a/config/species/caenorhabditis/caenorhabditis_parameters.cfg b/config/species/caenorhabditis/caenorhabditis_parameters.cfg index cdfefd67..d4588774 100644 --- a/config/species/caenorhabditis/caenorhabditis_parameters.cfg +++ b/config/species/caenorhabditis/caenorhabditis_parameters.cfg @@ -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 diff --git a/config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg b/config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg index f2fc2b69..0c44759b 100644 --- a/config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg +++ b/config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg @@ -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 diff --git a/config/species/chicken/chicken_parameters.cfg b/config/species/chicken/chicken_parameters.cfg index 92b7f8cc..d2406a8a 100644 --- a/config/species/chicken/chicken_parameters.cfg +++ b/config/species/chicken/chicken_parameters.cfg @@ -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 diff --git a/config/species/chiloscyllium/chiloscyllium_parameters.cfg b/config/species/chiloscyllium/chiloscyllium_parameters.cfg index 960601f2..9de9ce49 100644 --- a/config/species/chiloscyllium/chiloscyllium_parameters.cfg +++ b/config/species/chiloscyllium/chiloscyllium_parameters.cfg @@ -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 diff --git a/config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1 b/config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1 index f4aba6c0..b5ae0522 100644 --- a/config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1 +++ b/config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1 @@ -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 diff --git a/config/species/ciona/ciona_parameters.cfg b/config/species/ciona/ciona_parameters.cfg index f07c6896..95bea3f0 100644 --- a/config/species/ciona/ciona_parameters.cfg +++ b/config/species/ciona/ciona_parameters.cfg @@ -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 diff --git a/config/species/ciona/ciona_parameters.cfg.orig1 b/config/species/ciona/ciona_parameters.cfg.orig1 index 19bce2a2..9a0ed15e 100644 --- a/config/species/ciona/ciona_parameters.cfg.orig1 +++ b/config/species/ciona/ciona_parameters.cfg.orig1 @@ -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 diff --git a/config/species/coyote_tobacco/coyote_tobacco_parameters.cfg b/config/species/coyote_tobacco/coyote_tobacco_parameters.cfg index 882a4562..9378dc72 100644 --- a/config/species/coyote_tobacco/coyote_tobacco_parameters.cfg +++ b/config/species/coyote_tobacco/coyote_tobacco_parameters.cfg @@ -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 diff --git a/config/species/elephant_shark/elephant_shark_parameters.cfg b/config/species/elephant_shark/elephant_shark_parameters.cfg index 1b99d218..5702da66 100644 --- a/config/species/elephant_shark/elephant_shark_parameters.cfg +++ b/config/species/elephant_shark/elephant_shark_parameters.cfg @@ -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 diff --git a/config/species/fly/fly_parameters.cfg b/config/species/fly/fly_parameters.cfg index 7f946cdd..bdb7effc 100644 --- a/config/species/fly/fly_parameters.cfg +++ b/config/species/fly/fly_parameters.cfg @@ -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 diff --git a/config/species/fly_exp/fly_exp_parameters.cfg b/config/species/fly_exp/fly_exp_parameters.cfg index 6b017b6e..739093b5 100644 --- a/config/species/fly_exp/fly_exp_parameters.cfg +++ b/config/species/fly_exp/fly_exp_parameters.cfg @@ -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 diff --git a/config/species/generic/generic_parameters.cfg b/config/species/generic/generic_parameters.cfg index 158fe111..4234d250 100644 --- a/config/species/generic/generic_parameters.cfg +++ b/config/species/generic/generic_parameters.cfg @@ -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 diff --git a/config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg b/config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg index a0fce9ec..358d4011 100644 --- a/config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg +++ b/config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg @@ -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 diff --git a/config/species/honeybee1/honeybee1_parameters.cfg b/config/species/honeybee1/honeybee1_parameters.cfg index 983d661e..5e1d8852 100644 --- a/config/species/honeybee1/honeybee1_parameters.cfg +++ b/config/species/honeybee1/honeybee1_parameters.cfg @@ -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 diff --git a/config/species/honeybee1/honeybee1_parameters.cfg.orig1 b/config/species/honeybee1/honeybee1_parameters.cfg.orig1 index bdcec349..35c40650 100644 --- a/config/species/honeybee1/honeybee1_parameters.cfg.orig1 +++ b/config/species/honeybee1/honeybee1_parameters.cfg.orig1 @@ -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 diff --git a/config/species/japaneselamprey/japaneselamprey_parameters.cfg b/config/species/japaneselamprey/japaneselamprey_parameters.cfg index d60c8212..162e6e77 100644 --- a/config/species/japaneselamprey/japaneselamprey_parameters.cfg +++ b/config/species/japaneselamprey/japaneselamprey_parameters.cfg @@ -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 diff --git a/config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg b/config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg index 2b950afb..28d4ecc3 100644 --- a/config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg +++ b/config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg @@ -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 diff --git a/config/species/maize/maize_parameters.cfg b/config/species/maize/maize_parameters.cfg index 06832603..02516c28 100644 --- a/config/species/maize/maize_parameters.cfg +++ b/config/species/maize/maize_parameters.cfg @@ -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 diff --git a/config/species/maize5/maize5_parameters.cfg b/config/species/maize5/maize5_parameters.cfg index cb40ff6d..a58a1e81 100644 --- a/config/species/maize5/maize5_parameters.cfg +++ b/config/species/maize5/maize5_parameters.cfg @@ -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 diff --git a/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg b/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg index 05c1f425..9edd7098 100644 --- a/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg +++ b/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg @@ -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 diff --git a/config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg b/config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg index c6d51d88..7ab81385 100644 --- a/config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg +++ b/config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg @@ -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 diff --git a/config/species/parasteatoda/parasteatoda_parameters.cfg b/config/species/parasteatoda/parasteatoda_parameters.cfg index f291189c..08f2280e 100644 --- a/config/species/parasteatoda/parasteatoda_parameters.cfg +++ b/config/species/parasteatoda/parasteatoda_parameters.cfg @@ -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 diff --git a/config/species/pfalciparum/pfalciparum_parameters.cfg b/config/species/pfalciparum/pfalciparum_parameters.cfg index e7273660..6901dd6c 100644 --- a/config/species/pfalciparum/pfalciparum_parameters.cfg +++ b/config/species/pfalciparum/pfalciparum_parameters.cfg @@ -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 diff --git a/config/species/pisaster/pisaster_parameters.cfg b/config/species/pisaster/pisaster_parameters.cfg index 8cec1a86..19723a50 100644 --- a/config/species/pisaster/pisaster_parameters.cfg +++ b/config/species/pisaster/pisaster_parameters.cfg @@ -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 diff --git a/config/species/rhincodon/rhincodon_parameters.cfg b/config/species/rhincodon/rhincodon_parameters.cfg index daa07a66..ded819fa 100644 --- a/config/species/rhincodon/rhincodon_parameters.cfg +++ b/config/species/rhincodon/rhincodon_parameters.cfg @@ -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 diff --git a/config/species/rhincodon/rhincodon_parameters.cfg.orig1 b/config/species/rhincodon/rhincodon_parameters.cfg.orig1 index 20e8b802..ea20cd95 100644 --- a/config/species/rhincodon/rhincodon_parameters.cfg.orig1 +++ b/config/species/rhincodon/rhincodon_parameters.cfg.orig1 @@ -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 diff --git a/config/species/rhodnius/rhodnius_parameters.cfg b/config/species/rhodnius/rhodnius_parameters.cfg index ec7fac5c..c3db6d2b 100644 --- a/config/species/rhodnius/rhodnius_parameters.cfg +++ b/config/species/rhodnius/rhodnius_parameters.cfg @@ -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 diff --git a/config/species/rice/rice_parameters.cfg b/config/species/rice/rice_parameters.cfg index 6828462d..34842fad 100644 --- a/config/species/rice/rice_parameters.cfg +++ b/config/species/rice/rice_parameters.cfg @@ -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 diff --git a/config/species/s_aureus/s_aureus_parameters.cfg b/config/species/s_aureus/s_aureus_parameters.cfg index 56ce92fd..c4b5aa3c 100644 --- a/config/species/s_aureus/s_aureus_parameters.cfg +++ b/config/species/s_aureus/s_aureus_parameters.cfg @@ -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 diff --git a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg index 6c699150..56740853 100644 --- a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg +++ b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg @@ -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 diff --git a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1 b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1 index 3201e9ba..2a10a690 100644 --- a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1 +++ b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1 @@ -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 diff --git a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2 b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2 index e1b4a75a..9fa954f2 100644 --- a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2 +++ b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2 @@ -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 diff --git a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3 b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3 index 16b11052..dd3fccb9 100644 --- a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3 +++ b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3 @@ -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 diff --git a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4 b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4 index b96e6157..a5abb85e 100644 --- a/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4 +++ b/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4 @@ -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 diff --git a/config/species/schistosoma2/schistosoma2_parameters.cfg b/config/species/schistosoma2/schistosoma2_parameters.cfg index d7715503..9ed02706 100644 --- a/config/species/schistosoma2/schistosoma2_parameters.cfg +++ b/config/species/schistosoma2/schistosoma2_parameters.cfg @@ -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 diff --git a/config/species/scyliorhinus/scyliorhinus_parameters.cfg b/config/species/scyliorhinus/scyliorhinus_parameters.cfg index 1240ee9f..c049cb4f 100644 --- a/config/species/scyliorhinus/scyliorhinus_parameters.cfg +++ b/config/species/scyliorhinus/scyliorhinus_parameters.cfg @@ -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 diff --git a/config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1 b/config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1 index 03623ed9..131ec1d4 100644 --- a/config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1 +++ b/config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1 @@ -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 diff --git a/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg b/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg index 03a2651a..cc2108cc 100644 --- a/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg +++ b/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg @@ -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 diff --git a/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg b/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg index 0bb85611..47c46c58 100644 --- a/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg +++ b/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg @@ -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 diff --git a/config/species/template_prokaryotic/template_prokaryotic_parameters.cfg b/config/species/template_prokaryotic/template_prokaryotic_parameters.cfg index de5c9b6d..1c87f69b 100644 --- a/config/species/template_prokaryotic/template_prokaryotic_parameters.cfg +++ b/config/species/template_prokaryotic/template_prokaryotic_parameters.cfg @@ -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 diff --git a/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg b/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg index d2e81540..c1e10bab 100644 --- a/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg +++ b/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg @@ -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 diff --git a/config/species/tomato/tomato_parameters.cfg b/config/species/tomato/tomato_parameters.cfg index 701c8db8..c9fdb3e5 100644 --- a/config/species/tomato/tomato_parameters.cfg +++ b/config/species/tomato/tomato_parameters.cfg @@ -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 diff --git a/config/species/toxoplasma/toxoplasma_parameters.cfg b/config/species/toxoplasma/toxoplasma_parameters.cfg index 1cb22345..bfcf8383 100644 --- a/config/species/toxoplasma/toxoplasma_parameters.cfg +++ b/config/species/toxoplasma/toxoplasma_parameters.cfg @@ -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 diff --git a/config/species/trichinella/trichinella_parameters.cfg b/config/species/trichinella/trichinella_parameters.cfg index d7c8c6ef..087c9e7b 100644 --- a/config/species/trichinella/trichinella_parameters.cfg +++ b/config/species/trichinella/trichinella_parameters.cfg @@ -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 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 a69644a9..29c886ec 100644 --- a/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_parameters.cfg +++ b/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_parameters.cfg @@ -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 diff --git a/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg b/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg index 3dc4f3b6..380e31f0 100644 --- a/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg +++ b/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg @@ -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 diff --git a/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1 b/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1 index 1b088203..367bfe73 100644 --- a/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1 +++ b/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1 @@ -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 diff --git a/config/species/volvox/volvox_parameters.cfg b/config/species/volvox/volvox_parameters.cfg index e0343a3c..fa8087ad 100644 --- a/config/species/volvox/volvox_parameters.cfg +++ b/config/species/volvox/volvox_parameters.cfg @@ -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 diff --git a/config/species/wheat/wheat_parameters.cfg b/config/species/wheat/wheat_parameters.cfg index 74789340..b64ac1be 100644 --- a/config/species/wheat/wheat_parameters.cfg +++ b/config/species/wheat/wheat_parameters.cfg @@ -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 diff --git a/config/species/zebrafish/zebrafish_parameters.cfg b/config/species/zebrafish/zebrafish_parameters.cfg index 9d7297ed..0fbb7a29 100644 --- a/config/species/zebrafish/zebrafish_parameters.cfg +++ b/config/species/zebrafish/zebrafish_parameters.cfg @@ -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