Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 20:76f586562e8d draft

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author greg
date Mon, 01 May 2017 11:07:27 -0400
parents 33d615104dad
children a42b4450fd2a
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19:33d615104dad 20:76f586562e8d
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138 **Required options** 138 **Required options**
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140 * **Classified orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyClassifier tool selected from your history. Depending on how the GeneFamilyClassifier tool was exectured, these could either be proteins or proteins and their corresponding coding sequences. 140 * **Classified orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyClassifier tool selected from your history. Depending on how the GeneFamilyClassifier tool was exectured, these could either be proteins or proteins and their corresponding coding sequences.
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142 - **Proteins orthogroup fasta files** - proteins fasta files. 142 * **Codon alignments** - select 'Yes' to create codon multiple sequence alignments. This option requires protein and their corresponding coding sequences to be provided as input data.
143 - **Protein and coding sequences orthogroup fasta files** - proteins and their corresponding coding sequences fasta files.
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145 - **Construct orthogroup multiple codon alignments** - construct orthogroup multiple codon alignments.
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147 * **Multiple sequence alignment method** - method for estimating orthogroup multiple sequence alignments. PlantTribes estimates alignments using either MAFFT's L-INS-i algorithm or the divide and conquer approach implemented in the PASTA pipeline for large alignments. 144 * **Multiple sequence alignment method** - method for estimating orthogroup multiple sequence alignments. PlantTribes estimates alignments using either MAFFT's L-INS-i algorithm or the divide and conquer approach implemented in the PASTA pipeline for large alignments.
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149 - **MAFFT** - MAFFT algorithm. 146 - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations.
150 - **PASTA** - PASTA algorithm.
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152 - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations.
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154 **Other options** 148 **Other options**
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156 * **Alignment post-processing configuration** - select 'Yes' to enable multiple sequence alignment post-processing configuration options. 150 * **Alignment post-processing configuration** - select 'Yes' to enable multiple sequence alignment post-processing configuration options.
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158 - **Trimming method** - multiple sequence alignment trimming method. PlantTribes trims alignments using two automated approaches implemented in trimAl. Gap score based trimming removes alignments sites that do not achieve a user specified gap score. For example, a setting of 0.1 removes sites that have gaps in 90% or more of the sequences in the multiple sequence alignment. The automated heuristic trimming approach determines the best automated trimAl method to trim a given alignment as described in the trimAl tutorial `trimAl`_. 152 - **Trimming method** - multiple sequence alignment trimming method. PlantTribes trims alignments using two automated approaches implemented in trimAl. Gap score based trimming removes alignments sites that do not achieve a user specified gap score. For example, a setting of 0.1 removes sites that have gaps in 90% or more of the sequences in the multiple sequence alignment. The automated heuristic trimming approach determines the best automated trimAl method to trim a given alignment as described in the trimAl tutorial `trimAl`_.
159 - **Nucleotide based**
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161 - **Gap score** - 1.0 - (the fraction of sequences with gap allowed in an alignment site). The score is restricted to the range 0.0 - 1.0. Zero value has no effect. 154 - **Gap score** - 1.0 - (the fraction of sequences with gap allowed in an alignment site). The score is restricted to the range 0.0 - 1.0. Zero value has no effect.
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163 - **Remove sequences** - select 'Yes' to remove sequences in multiple sequence alignments that do not achieve a user specified alignment coverage score. For example, a setting of 0.7 removes sequences with more than 30% gaps in the alignment. This option requires one of the trimming methods to be set. 156 - **Remove sequences** - select 'Yes' to remove sequences in multiple sequence alignments that do not achieve a user specified alignment coverage score. For example, a setting of 0.7 removes sequences with more than 30% gaps in the alignment. This option requires one of the trimming methods to be set.
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