X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FRIO.wiki;h=30051ea7e03e294c65bd7c09b504d05d7444996b;hb=dcf877d3b3055f11e090023903a2571a08d939db;hp=a5965ba2fabbc363c18c668dbed637221d5d17c4;hpb=8df2f67b2c9e33933def4529c42649f88ae44a3d;p=jalview.git

diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki
index a5965ba..30051ea 100644
--- a/wiki/RIO.wiki
+++ b/wiki/RIO.wiki
@@ -13,23 +13,27 @@ java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene tre
 }}}
 
 === Options ===
-
-  * -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 ====
 The gene trees ideally are in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format, with taxonomy and sequence data in appropriate fields; but can also be in New Hamphshire (Newick) or Nexus format, as long as species information can be extracted from the gene names (e.g. "HUMAN" from "BCL2_HUMAN") ([http://forester.googlecode.com/files/gene_trees_rio.nh example]).
-All gene trees must be completely binary.
+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 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. 
 
 
-=== 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`
 
 === Example files ===
   * [http://forester.googlecode.com/files/gene_trees_rio.nh gene trees file]