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.
12 java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene trees> <species tree> <outfile> [logfile]
17 * -b : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed)
21 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]).
22 All gene trees must be *completely binary*.
25 ==== Species tree ====
26 Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species_tree_rio.xml example]).
27 The species tree is allowed to have nodes with more than two descendents (polytomies) as long as GSDIR ([GSDI GSDI] re-rooting) algorithm is used.
31 `rio gene_trees.nh species.xml outtable.tsv log.txt`
35 * [http://forester.googlecode.com/files/gene_trees_rio.nh gene trees file]
36 * [http://forester.googlecode.com/files/species_tree_rio.xml species tree file]
41 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]
43 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]
45 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]
50 Download forester.jar here: http://code.google.com/p/forester/downloads/list