X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FRIO.wiki;h=21de730628be95765d9f6c186b8a34fa20aa707d;hb=c3f7a7af2eeb49f8847b5b955c8960097257228e;hp=eb368e693a27a20eeb5db253eaba16c098146fb1;hpb=5a655d5fbaaac8857f9c19a6ba375f76a5f894d5;p=jalview.git

diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki
index eb368e6..21de730 100644
--- a/wiki/RIO.wiki
+++ b/wiki/RIO.wiki
@@ -8,16 +8,15 @@ 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> <species tree> <outfile> [logfile]
-}}}
+
+`java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene trees> <species tree> <outfile> [logfile]`
 
 === Options ===
-  * `-f=<first>` : first gene tree to analyze (0-based index)
-  * `-l=<last>` : last gene tree to analyze (0-based index)
+  * `-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) 
+  * `-b` : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed, as are all options) 
 
   
 ==== Gene trees ====
@@ -30,9 +29,16 @@ The species tree ideally is in [http://www.biomedcentral.com/1471-2105/10/356/ p
 The species tree is allowed to have nodes with more than two descendants (polytomies), as long as the (slower) GSDIR ([GSDI GSDI] re-rooting) algorithm is used. 
 
 
-=== Example ===
+==== Note about memory ====
+Since the Java memory default allocation is too small for even moderately large data-sets, it is necessary to increase it with the `-Xmx2048m` command line option.
+
+
+=== Examples ===
 `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`
+
+`rio gene_trees.nh species.xml outtable.tsv log.txt -f=0 -l=49`
 
 === Example files ===
   * [http://forester.googlecode.com/files/gene_trees_rio.nh gene trees file]