Mercurial > repos > greg > phylogenomics_analysis

changeset 15:34aa10ba20ef draft

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Uploaded
author greg
date Fri, 06 Jan 2017 14:14:12 -0500
parents a8a4f6009451
children 4bb89dcc9642
files phylogenomics_analysis.xml
diffstat 1 files changed, 4 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/phylogenomics_analysis.xml	Fri Jan 06 13:58:59 2017 -0500
+++ b/phylogenomics_analysis.xml	Fri Jan 06 14:14:12 2017 -0500
@@ -309,6 +309,7 @@
  - **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 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.
@@ -318,7 +319,9 @@
 
 * **MSA quality control options**
 
- - **Remove gappy sequences in alignments?** - Removes gappy sites in alignments (e.g. 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).
 
     </help>
     <citations>