#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 file> <species tree file> [outfile]
}}}
=== Options ===

  * -co: cutoff for ortholog output (default: 50) 
  
  * -t : file-name for output table of all vs. all ortholgy support
  
  * -q : name for query (sequence/node), if this is used, `[`outfile`]` is required as well

  * -s : sort (default: 2)

  * -u : to output ultra-paralogs (species specific expansions/paralogs)

  * -cu: cutoff for ultra-paralog output (default: 50)

==== Note ====

Either output of all vs. all ortholgy support with -t=`<`output table`>`and/or output for 
one query sequence with -q and a  `[`outfile`]` are required.

==== Sort ====

  * 0: orthologies
  * 1: orthologies > super orthologies
  * 2: super orthologies > orthologies

==== 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").

==== Species tree ====
Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species.xml example]).


=== Examples ===
`rio gene_trees.nh species.xml outfile -q=BCL2_HUMAN -t=outtable -u -cu=60 -co=60`

`rio gene_trees.nh species.xml -t=outtable`


<wiki:comment>
=== Example files ===
  * [http://forester.googlecode.com/files/wnt_gene_tree.xml gene tree]
  * [http://forester.googlecode.com/files/species.xml species tree]
  * [http://forester.googlecode.com/files/wnt_gsdi_log.txt log file (output)]
</wiki:comment>

== 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