X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FRIO.wiki;h=8bafb64c0a51ea3fe2cdbc47689d65d8ad857f19;hb=bfd17a215d89bce322b5d77163f0d1d6cedb390c;hp=c9b71af2e22b4e468218445be97fdc06cb6b546a;hpb=4c7bfc9953191df22b048864a37540b6b696326c;p=jalview.git

diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki
index c9b71af..8bafb64 100644
--- a/wiki/RIO.wiki
+++ b/wiki/RIO.wiki
@@ -6,56 +6,43 @@
 
 RIO (Resampled Inference of Orthologs) is a method for automated phylogenomics based on explicit phylogenetic inference. RIO analyses are performed over resampled phylogenetic trees to estimate the reliability of orthology assignments.
 
+
 == Usage == 
 {{{
-java -Xmx1024m -cp
-path/to/forester.jar org.forester.application.rio [options] <gene trees file> <species tree file> [outfile]
+java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene trees> <species tree> <outfile> [logfile]
 }}}
-=== Options ===
-
-  * -co: cutoff for ortholog output (default: 50) 
-  
-  * -t : file-name for output table
-  
-  * -q : name for query (sequence/node)
-
-  * -s : sort (default: 2)
-
-  * -u : to output ultra-paralogs (species specific expansions/paralogs)
 
-  * -cu: cutoff for ultra-paralog output (default: 50)
-
-==== Sort ====
+=== Options ===
 
-  * 0: orthologies
-  * 1: orthologies > super orthologies
-  * 2: super orthologies > orthologies
+  * -b : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed) 
 
+  
 ==== Gene trees ====
-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").
+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*.
 
-==== Species tree ====
-Must be in phyloXML format  ([http://forester.googlecode.com/files/species.xml example]).
 
+==== 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. 
 
-=== Examples ===
-`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`
+=== Example ===
+`rio gene_trees.nh species.xml outtable.tsv log.txt`
 
 
-<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]
+  
 
 == References ==
 
 Zmasek CM and Eddy SR "RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs" [http://www.biomedcentral.com/1471-2105/3/14/ BMC Bioinformatics 2002, 3:14]
 
 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]
+
+Han M and Zmasek CM "phyloXML: XML for evolutionary biology and comparative genomics" [http://www.biomedcentral.com/1471-2105/10/356/ BMC Bioinformatics 2009, 10:356]
  
 
 == Download ==