#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 -Xmx2048m -cp 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 of all vs. all ortholgy support
-
- * -q : name for query (sequence/node), if this is used, `[`outfile`]` is required as well
-
- * -s : sort (default: 2)
-
- * -u : to output ultra-paralogs (species specific expansions/paralogs)
-
- * -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 and a `[`outfile`]` are required.
-
-==== Sort ====
-
- * 0: orthologies
- * 1: orthologies > super orthologies
- * 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") ([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_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`
-
-
-=== Example files ===
- * [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 ==
-
-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 ==
-
-Download forester.jar here: http://code.google.com/p/forester/downloads/list
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