# HG changeset patch
# User greg
# Date 1493651664 14400
# Node ID a42b4450fd2acdd754614cd662ffd5379cb99571
# Parent  5b42773159d8477523e4a13e2e9b3c282388c207
Uploaded

diff -r 5b42773159d8 -r a42b4450fd2a gene_family_aligner.xml
--- a/gene_family_aligner.xml	Mon May 01 11:07:40 2017 -0400
+++ b/gene_family_aligner.xml	Mon May 01 11:14:24 2017 -0400
@@ -151,13 +151,13 @@
 
   - **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`_.
 
-      - **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.
+    - **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.
 
   - **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.
 
-      - **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.
+    - **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.
 
-      - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences.  Zero value has no effect.
+    - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences.  Zero value has no effect.
 
 .. _trimAl: http://trimal.cgenomics.org