Mercurial > repos > greg > kaks_analysis

changeset 29:c91e1673c8e7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Mon, 01 May 2017 12:41:26 -0400
parents b807167c1e60
children 715ca3160a27
files kaks_analysis.xml
diffstat 1 files changed, 6 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/kaks_analysis.xml	Fri Apr 28 14:30:26 2017 -0400
+++ b/kaks_analysis.xml	Mon May 01 12:41:26 2017 -0400
@@ -207,19 +207,19 @@
 
  * **Required**
 
-  - **Coding sequences for the first species** - coding sequence fasta file for for the first species either produced by the AssemblyPostProcessor tool or an external source selected from your history.
-  - **Protein sequences for the first species** - corresponding protein sequence fasta files for the first species either produced by the AssemblyPostProcessor tool or an external source selected from your history.
-  - **Type of sequence comparison** - pairwise sequence comparison to determine homolgous pairs.  This can be either paralogous for self-species comparison or orthologous for cross-species comparison.  Cross species comparision requires data selected for the second species.
+  - **Coding sequences for the first species** - coding sequence fasta file for the first species either produced by the AssemblyPostProcessor tool or from an external source selected from your history.
+  - **Protein sequences for the first species** - corresponding protein sequence fasta files for the first species either produced by the AssemblyPostProcessor tool or from an external source selected from your history.
+  - **Type of sequence comparison** - pairwise sequence comparison to determine homolgous pairs.  This can be either paralogous for self-species comparison or orthologous for cross-species comparison.  Cross-species comparision requires input for the second species.
 
  * **Optional**
 
-  - **Coding sequences for the second species** - coding sequence fasta file for for the second species either produced by the AssemblyPostProcessor tool or an external source selected from your history.  Required only for orthologous comparison.
-  - **Protein sequences for the second species** - corresponding protein sequence fasta files for the second species either produced by the AssemblyPostProcessor tool or an external source selected from your history.  Required only for orthologous comparison.
+  - **Coding sequences for the second species** - coding sequence fasta file for the second species either produced by the AssemblyPostProcessor tool or from an external source selected from your history.  This option is required only for orthologous comparison.
+  - **Protein sequences for the second species** - corresponding protein sequence fasta files for the second species either produced by the AssemblyPostProcessor tool or from an external source selected from your history.  This option is required only for orthologous comparison.
   - **Alignment coverage configuration** - select 'Yes' to set the minimum allowable alignment coverage length between homologous pairs.  PlantTribes uses global codon alignment match score to determine the pairwise alignment coverage.  By default, the match score is set to 0.5 if 'No' is selected.
 
     - **match score** - number of base matches in a pairwise sequence alignment divided by the length of shorter sequence.  Positions in the alignment corresponding to gaps are not considered.  The score is restricted to the range 0.3 - 1.0.
 
-  - **Species rates recalibration configuration** - select 'Yes' to recalibrate synonymous substitution rates of a species using a predetermined evolutionary rate.  Recalibration evolutionary rate can be determined from a species tree inferred from a collection of conserved single copy genes from taxa of interest as described in Cui et al., 2006.  Applies only to paralogous comparisons.
+  - **Species rates recalibration configuration** - select 'Yes' to recalibrate synonymous substitution rates of a species using a predetermined evolutionary rate.  Recalibration evolutionary rate can be determined from a species tree inferred from a collection of conserved single copy genes from taxa of interest as described in Cui et al., 2006.  Rate recalibration applies only to paralogous comparisons.
 
     - **recalibration rate** - a predetermined evolutionary recalibration rate.