Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 22:a42b4450fd2a draft

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author greg
date Mon, 01 May 2017 11:14:24 -0400
parents 76f586562e8d
children 4bc180041705
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21:5b42773159d8 22:a42b4450fd2a
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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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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`_. 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`_.
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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. 154 - **Gap score** - 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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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. 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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158 - **Coverage score** - minimum fraction of sites without gaps for a sequence in a multiple sequence alignment. The score is restricted to the range 0.0 - 1.0. Zero value has no effect. 158 - **Coverage score** - minimum fraction of sites without gaps for a sequence in a multiple sequence alignment. The score is restricted to the range 0.0 - 1.0. Zero value has no effect.
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160 - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences. Zero value has no effect. 160 - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences. Zero value has no effect.
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162 .. _trimAl: http://trimal.cgenomics.org 162 .. _trimAl: http://trimal.cgenomics.org
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164 </help> 164 </help>
165 <citations> 165 <citations>