X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FRIO.wiki;h=21de730628be95765d9f6c186b8a34fa20aa707d;hb=430a62fbc15e1ddf9fdda748786cfeb43620255a;hp=8bafb64c0a51ea3fe2cdbc47689d65d8ad857f19;hpb=d7382727d73ce56aa0382b24b755d659521efa23;p=jalview.git

diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki
index 8bafb64..21de730 100644
--- a/wiki/RIO.wiki
+++ b/wiki/RIO.wiki
@@ -8,13 +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]
-}}}
 
-=== Options ===
+`java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene trees> <species tree> <outfile> [logfile]`
 
-  * -b : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed) 
+=== Options ===
+  * `-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, as are all options) 
 
   
 ==== Gene trees ====
@@ -23,13 +25,20 @@ 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 the (slower) GSDIR ([GSDI GSDI] re-rooting) algorithm is used. 
+The species tree ideally is in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format, but can also be in New Hamphshire (Newick) or Nexus format  ([http://forester.googlecode.com/files/species_tree_rio.xml example]). 
+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. 
+
 
+==== 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.
 
-=== Example ===
+
+=== 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]