From 59f0ecb2543aa7a29594a93fe117ffc545a6a4f4 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 23 May 2014 23:50:00 +0000 Subject: [PATCH] Edited wiki page RIO through web user interface. --- wiki/RIO.wiki | 58 +-------------------------------------------------------- 1 file changed, 1 insertion(+), 57 deletions(-) diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki index 6209ad7..1aa1e54 100644 --- a/wiki/RIO.wiki +++ b/wiki/RIO.wiki @@ -1,59 +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) (default: analyze all gene trees) - * `-l=` : last gene tree to analyze (0-based index) (default: analyze all gene trees) - * `-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, 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 \ No newline at end of file +https://sites.google.com/site/cmzmasek/home/software/forester/rio \ No newline at end of file -- 1.7.10.2