X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FRIO.wiki;h=1aa1e544ceda59630355e3216cf0a85f102aaac0;hb=d2823363d9efbad977b5029c09c27ee09a4cbece;hp=e14e5d1c6bb5a5e7eab08f2c85179222d3a8008c;hpb=a6bf619d06e064f2267586263723dbac73a42583;p=jalview.git

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 #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. 
-
-
-=== Example ===
-`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
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