Edited wiki page RIO through web user interface.

diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki
index 180a553..1cc4ada 100644 (file)
--- a/wiki/RIO.wiki
+++ b/wiki/RIO.wiki
@@ -32,37 +32,23 @@ path/to/forester.jar org.forester.application.rio [options] <gene trees file> <s
   * 2: super orthologies > orthologies
 
 ==== Gene trees ====
-The gene trees ideally are in phyloXML, 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 phyloXML,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").
 
 ==== Species tree ====
 Must be in phyloXML format  ([http://forester.googlecode.com/files/species.xml example]).
 
-=== Output ===
-
-Besides the main output of a gene tree with duplications and speciations assigned to all of its internal nodes, this program also produces the following:
-  * a log file, ending in `"_gsdi_log.txt"` ([http://forester.googlecode.com/files/wnt_gsdi_log.txt example])
-  * a species tree file which only contains external nodes with were needed for the reconciliation, ending in `"_species_tree_used.xml"`
-  * if the gene tree contains species with scientific species names such as "Pyrococcus horikoshii strain ATCC 700860" and if a mapping cannot be establish based on these, GSDI will attempt to map by removing the "strain" (or "subspecies") information, these will be listed in a file ending in `"_gsdi_remapped.txt"`.
-
-=== Taxonomic mapping between gene and species tree ===
-
-GSDI can establish a taxonomic mapping between gene and species tree on the following three data fields:
-  * scientific names (e.g. "Pyrococcus horikoshii")
-  * taxonomic identifiers (e.g. "35932" from uniprot or ncbi)
-  * taxonomy codes (e.g. "PYRHO") 
-
-
 
 === Example ===
-`gsdi -g -q gene_tree.xml tree_of_life.nwk out.xml`
+`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>
 
 == References ==
 
@@ -71,7 +57,6 @@ Zmasek CM and Eddy SR "RIO: Analyzing proteomes by automated phylogenomics using
 Zmasek CM and Eddy SR "A simple algorithm to infer gene duplication and speciation events on a gene tree" [http://bioinformatics.oxfordjournals.org/content/17/9/821.abstract Bioinformatics, 17, 821-828]
  
 
-
 == Download ==
 
 Download forester.jar here: http://code.google.com/p/forester/downloads/list
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