X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FRIO.wiki;h=1aa1e544ceda59630355e3216cf0a85f102aaac0;hb=d2823363d9efbad977b5029c09c27ee09a4cbece;hp=79c40b7a6fb20e42794321c0552a19a7947a11d9;hpb=1a8cad845aa24435505aff7998bf9a90697202ac;p=jalview.git diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki index 79c40b7..1aa1e54 100644 --- a/wiki/RIO.wiki +++ b/wiki/RIO.wiki @@ -1,53 +1,3 @@ #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] [logfile] -}}} - -=== Options === - * -f= : first gene tree to analyze (0-based index) - * -l= : last gene tree to analyze (0-based index) - * -r= : re-rooting method for gene trees, possible values or 'none', 'midpoint', or 'outgroup' (default: by minizming duplications) - * -o= : 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` - - -=== 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 \ No newline at end of file +https://sites.google.com/site/cmzmasek/home/software/forester/rio \ No newline at end of file