Edited wiki page RIO through web user interface.

[jalview.git] / wiki / RIO.wiki

diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki
index 79c40b7..e14e5d1 100644 (file)
--- a/wiki/RIO.wiki
+++ b/wiki/RIO.wiki
@@ -13,11 +13,11 @@ java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene tre
 }}}
 
 === Options ===
-  * -f=<first> : first gene tree to analyze (0-based index)
-  * -l=<last> : last gene tree to analyze (0-based index)
-  * -r=<re-rooting> : re-rooting method for gene trees, possible values or 'none', 'midpoint', or 'outgroup' (default: by minizming duplications)
-  * -o=<outgroup>  : for rooting by outgroup, name of outgroup (external gene tree node)
-  * -b : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed) 
+  * `-f=<first>` : first gene tree to analyze (0-based index) (default: analyze all gene trees)
+  * `-l=<last>` : last gene tree to analyze (0-based index) (default: analyze all gene trees)
+  * `-r=<re-rooting>` : re-rooting method for gene trees, possible values or 'none', 'midpoint', or 'outgroup' (default: by minizming duplications)
+  * `-o=<outgroup>` : for rooting by outgroup, name of outgroup (external gene tree node)
+  * `-b` : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed) 
 
   
 ==== Gene trees ====
@@ -33,6 +33,7 @@ The species tree is allowed to have nodes with more than two descendants (polyto
 === Example ===
 `rio gene_trees.nh species.xml outtable.tsv log.txt`
 
+`rio gene_trees.nh species.xml outtable.tsv log.txt -r=outgroup -o=XVL1_ECOLI`
 
 === Example files ===
   * [http://forester.googlecode.com/files/gene_trees_rio.nh gene trees file]