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+#summary resampled inference of orthologs
+
+= RIO: Resampled Inference of Orthologs =
+
+== Purpose ==
+
+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]
+}}}
+=== 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 ====
+
+  * 0: orthologies
+  * 1: orthologies > super orthologies
+  * 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").
+
+==== 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`
+
+
+=== 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)]
+
+
+== 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]
+ 
+
+
+== Download ==
+
+Download forester.jar here: http://code.google.com/p/forester/downloads/list
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