Mercurial > repos > greg > phylogenomics_analysis

changeset 17:7a6c7f3f9637 draft

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Uploaded
author greg
date Fri, 06 Jan 2017 14:17:14 -0500
parents 4bb89dcc9642
children 7d622f6a4732
files phylogenomics_analysis.xml
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/phylogenomics_analysis.xml	Fri Jan 06 14:15:40 2017 -0500
+++ b/phylogenomics_analysis.xml	Fri Jan 06 14:17:14 2017 -0500
@@ -300,7 +300,7 @@
  - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
  - **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL.
 
- * **Multiple sequence alignments options**
+* **Multiple sequence alignments options**
 
  - **Select process for multiple sequence alignments** - Process used for setting multiple sequence alignments.
  - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create orthogroup fasta files?' option on the GeneFamilyClassifier tool when generating the selected input.  This tool will produce an error if 'No' was selected.
@@ -308,14 +308,14 @@
  - **Sequence type used in the phylogenetic inference** - Sequence type used in the phylogenetic inference.
  - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create corresponding coding sequences?' option on the GeneFamilyClassifier tool when generating the selected input.  This tool will produce an error if 'No' was selected.
 
- * **Phylogenetic trees options**
+* **Phylogenetic trees options**
 
  - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
  - **Select history item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees?** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
  - **History item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees** -History item containing a set of string fragments matching sequences identifiers of species in the classification (including scaffold taxa) to be used for determining the most basal taxa in the orthogroups for rooting trees. The set of string fragments must be listed in decreasing order from older to younger lineages.
  - **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
+ - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.
 
 * **MSA quality control options**