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]
16 * `-f=<first>` : first gene tree to analyze (0-based index)
17 * `-l=<last>` : last gene tree to analyze (0-based index)
18 * `-r=<re-rooting>` : re-rooting method for gene trees, possible values or 'none', 'midpoint', or 'outgroup' (default: by minizming duplications)
19 * `-o=<outgroup>` : for rooting by outgroup, name of outgroup (external gene tree node)
20 * `-b` : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed)
24 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]).
25 All gene trees must be *completely binary*.
28 ==== Species tree ====
29 The species tree ideally is in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format, but can also be in New Hamphshire (Newick) or Nexus format ([http://forester.googlecode.com/files/species_tree_rio.xml example]).
30 The species tree is allowed to have nodes with more than two descendants (polytomies), as long as the (slower) GSDIR ([GSDI GSDI] re-rooting) algorithm is used.
34 `rio gene_trees.nh species.xml outtable.tsv log.txt`
38 * [http://forester.googlecode.com/files/gene_trees_rio.nh gene trees file]
39 * [http://forester.googlecode.com/files/species_tree_rio.xml species tree file]
44 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]
46 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]
48 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]
53 Download forester.jar here: http://code.google.com/p/forester/downloads/list