1 #summary resampled inference of orthologs
3 = RIO: Resampled Inference of Orthologs =
7 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.
11 java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene trees file> <species tree file> [outfile]
15 * -co: cutoff for ortholog output (default: 50)
17 * -t : file-name for output table
19 * -q : name for query (sequence/node)
21 * -s : sort (default: 2)
23 * -u : to output ultra-paralogs (species specific expansions/paralogs)
25 * -cu: cutoff for ultra-paralog output (default: 50)
30 * 1: orthologies > super orthologies
31 * 2: super orthologies > orthologies
34 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").
36 ==== Species tree ====
37 Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species.xml example]).
41 `rio gene_trees.nh species.xml outfile -q=BCL2_HUMAN -t=outtable -u -cu=60 -co=60`
43 `rio gene_trees.nh species.xml -t=outtable`
48 * [http://forester.googlecode.com/files/wnt_gene_tree.xml gene tree]
49 * [http://forester.googlecode.com/files/species.xml species tree]
50 * [http://forester.googlecode.com/files/wnt_gsdi_log.txt log file (output)]
55 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]
57 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]
59 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]
64 Download forester.jar here: http://code.google.com/p/forester/downloads/list