X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FRIO.wiki;h=6d69e3caa0abfccbf809a5d068ff864766c70c18;hb=08bd889bc13de7415319ea7202d8afb27879c18d;hp=38a8660e43c0f5093938acab75e0126e28bf4a38;hpb=162f375cc97383cd18534716e81eeb724db28307;p=jalview.git

diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki
index 38a8660..6d69e3c 100644
--- a/wiki/RIO.wiki
+++ b/wiki/RIO.wiki
@@ -14,9 +14,9 @@ java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene tre
 
   * -co: cutoff for ortholog output (default: 50) 
   
-  * -t : file-name for output table
+  * -t : file-name for output table of all vs. all ortholgy support
   
-  * -q : name for query (sequence/node), if this is bing used, [outfile] is required as well
+  * -q : name for query (sequence/node), if this is used, `[`outfile`]` is required as well
 
   * -s : sort (default: 2)
 
@@ -24,6 +24,10 @@ java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene tre
 
   * -cu: cutoff for ultra-paralog output (default: 50)
 
+==== Note ====
+
+Either output of all vs. all ortholgy support with -t=`<`output table`>` and/or output for one query sequence with -q=`<`query name`>` and a  `[`outfile`]` are required.
+
 ==== Sort ====
 
   * 0: orthologies
@@ -31,24 +35,25 @@ java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene tre
   * 2: super orthologies > orthologies
 
 ==== 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").
+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]).
 
 ==== Species tree ====
-Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species.xml example]).
+Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species_tree_rio.xml example]).
 
 
 === Examples ===
+`rio gene_trees_rio.nh species_tree_rio.xml outfile -q=D_HUMAN -t=outtable -u -cu=10 -co=10`
+
 `rio gene_trees.nh species.xml outfile -q=BCL2_HUMAN -t=outtable -u -cu=60 -co=60`
 
 `rio gene_trees.nh species.xml -t=outtable`
 
 
-<wiki:comment>
 === Example files ===
-  * [http://forester.googlecode.com/files/wnt_gene_tree.xml gene tree]
-  * [http://forester.googlecode.com/files/species.xml species tree]
-  * [http://forester.googlecode.com/files/wnt_gsdi_log.txt log file (output)]
-</wiki:comment>
+  * [http://forester.googlecode.com/files/gene_trees_rio.nh gene trees file]
+  * [http://forester.googlecode.com/files/species_tree_rio.xml species tree file]
+  * [http://forester.googlecode.com/files/rio_outfile.txt output] (for query "D_HUMAN")
+
 
 == References ==