Edited wiki page RIO through web user interface.

[jalview.git] / wiki / RIO.wiki

diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki
index c595df2..107deca 100644 (file)
--- a/wiki/RIO.wiki
+++ b/wiki/RIO.wiki
@@ -9,7 +9,7 @@ RIO (Resampled Inference of Orthologs) is a method for automated phylogenomics b
 
 == Usage == 
 {{{
-java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene trees infile> <species tree infile> <all vs all orthology table outfile> [logfile]
+java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene trees> <species tree> <outfile> [logfile]
 }}}
 
 === Options ===
@@ -24,7 +24,7 @@ All gene trees must be completely binary.
 
 ==== Species tree ====
 Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species_tree_rio.xml example]). 
-The species tree is allowed to have nodes with more than two descendents (polytomies) as long as GSDIR (GSDI re-rooting) algorithm is used. 
+The species tree is allowed to have nodes with more than two descendents (polytomies) as long as GSDIR ([GSDI GSDI] re-rooting) algorithm is used. 
 
 
 === Example ===