#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) 

  
==== 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]).
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  ([http://forester.googlecode.com/files/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. 


=== 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`

=== 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]
  

== 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