Mercurial > repos > greg > phylogenomics_analysis
changeset 69:34dcfb570551 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 02 Mar 2017 10:08:10 -0500 |
| parents | 5f76ffe55d0f |
| children | bd26a18387ae |
| files | phylogenomics_analysis.xml |
| diffstat | 1 files changed, 4 insertions(+), 7 deletions(-) [+] |
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--- a/phylogenomics_analysis.xml Tue Feb 28 11:10:33 2017 -0500 +++ b/phylogenomics_analysis.xml Thu Mar 02 10:08:10 2017 -0500 @@ -13,9 +13,6 @@ </stdio> <command> <![CDATA[ - #import os - #import sys - #if str($options_type.options_type_selector) == 'advanced': #set multiple_sequence_alignments_cond = $options_type.multiple_sequence_alignments_cond #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments @@ -269,13 +266,13 @@ **Options** - * **Required options** + * **Required** - **Select gene family clusters** - Sequences classified into gene family clusters, optionally including corresponding coding sequences. - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data. - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters). - * **Multiple sequence alignments options** + * **Multiple sequence alignments** - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments. - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs'. @@ -283,7 +280,7 @@ - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference. - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs' or this tool will produce an error. - * **Phylogenetic trees options** + * **Phylogenetic trees** - **Phylogenetic trees inference method** - Phylogenetic trees inference method. - **Select rooting order configuration for rooting trees??** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup. @@ -291,7 +288,7 @@ - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments. - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments. - * **MSA quality control options** + * **MSA quality control** - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps). - **Select process used for gap trimming** - Either nucleotide based trimming or alignments are trimed using using trimAl's ML heuristic trimming approach.