# HG changeset patch
# User greg
# Date 1487163589 18000
# Node ID 963f84101cdc8f23086152111e057beebb228b28
# Parent 1b256588fb0663a9d570542d4a1987dee9bf5192
Uploaded
diff -r 1b256588fb06 -r 963f84101cdc phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml Mon Feb 13 09:33:37 2017 -0500
+++ b/phylogenomics_analysis.xml Wed Feb 15 07:59:49 2017 -0500
@@ -300,41 +300,42 @@
- This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
- complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
- analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the
- **Classify gene sequences into precomputed orthologous gene family clusters** tool.
+This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
+complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
+analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the
+**Classify gene sequences into precomputed orthologous gene family clusters** tool.
- -----
+-----
- **Options**
+**Options**
- * **Required options**
+ * **Required options**
- - **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**
+ - **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**
- - **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'.
- - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
- - **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.
+ - **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'.
+ - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
+ - **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 options**
- - **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.
- - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree.
- - **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.
+ - **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.
+ - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree.
+ - **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 options**
- - **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.
- - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps).
+ - **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.
+ - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps).