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fix typo recomment -> recommend
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@hmehlan
hmehlan committed Nov 7, 2018
1 parent 4afcc6a commit aee62ae
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Showing 71 changed files with 71 additions and 71 deletions.
2 changes: 1 addition & 1 deletion config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/E_coli_K12/E_coli_K12_parameters.cfg
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/adorsata/adorsata_parameters.cfg
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/b_pseudomallei/b_pseudomallei_parameters.cfg
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/cacao/cacao_parameters.cfg
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/caenorhabditis/caenorhabditis_parameters.cfg
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg
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Expand Up @@ -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
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