Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 23:4bc180041705 draft

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Uploaded
author greg
date Mon, 01 May 2017 14:02:13 -0400
parents a42b4450fd2a
children 6d34db10765c
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22:a42b4450fd2a 23:4bc180041705
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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 * **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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144 - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations.
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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. 146 * **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.
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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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146 - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations.
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148 **Other options** 148 **Other options**
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150 * **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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