#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> <species tree> <outfile> [logfile]`
-
-=== Options ===
- * `-f=<first>` : first gene tree to analyze (0-based index) (default: analyze all gene trees)
- * `-l=<last>` : last gene tree to analyze (0-based index) (default: analyze all gene trees)
- * `-r=<re-rooting>` : re-rooting method for gene trees, possible values or 'none', 'midpoint', or 'outgroup' (default: by minizming duplications)
- * `-o=<outgroup>` : for rooting by outgroup, name of outgroup (external gene tree node)
- * `-b` : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed, as are all options)
-
-
-==== 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") ([https://forester.googlecode.com/svn/forester/examples/rio/gene_trees_rio.nh example]).
-All gene trees must be *completely binary*.
-
-
-==== Species tree ====
-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 ([https://forester.googlecode.com/svn/forester/examples/rio/species_tree_rio.xml example]).
-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.
-
-
-==== Note about memory ====
-Since the Java memory default allocation is too small for even moderately large data-sets, it is necessary to increase it with the `-Xmx2048m` command line option.
-
-
-=== Examples ===
-`rio gene_trees.nh species.xml outtable.tsv log.txt`
-
-`rio gene_trees.nh species.xml outtable.tsv log.txt -r=outgroup -o=XVL1_ECOLI`
-
-`rio gene_trees.nh species.xml outtable.tsv log.txt -f=0 -l=49`
-
-=== Example files ===
- * [https://forester.googlecode.com/svn/forester/examples/rio/gene_trees_rio.nh gene trees file]
- * [https://forester.googlecode.com/svn/forester/examples/rio/species_tree_rio.xml species tree file]
-
-
-== 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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