From e4bf875e31684f3bae879bc1002fedc6fdec1984 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 28 Nov 2012 23:04:58 +0000 Subject: [PATCH] Edited wiki page rio through web user interface. --- wiki/rio.wiki | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/wiki/rio.wiki b/wiki/rio.wiki index 696bff1..ab4155c 100644 --- a/wiki/rio.wiki +++ b/wiki/rio.wiki @@ -4,22 +4,27 @@ == Purpose == -To infer duplication events on a gene tree given a trusted species tree. +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 -Xmx1024m -cp -path/to/forester.jar org.forester.application.rio [-options] +path/to/forester.jar org.forester.application.rio [options] [outfile] }}} === Options === - * -g: to allow stripping of gene tree nodes without a matching species in the species tree - - * -m: use most parimonious duplication model for GSDI: assign nodes as speciations which would otherwise be assiged as potential duplications due tp polytomies in the species tree + * -co: cutoff for ortholog output (default: 50) + + * -t : file-name for output table + + * -q : name for query (sequence/node) + + * -s : sort (default: 2) + + * -u : to output ultra-paralogs (species specific expansions/paralogs) - * -q: to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus) + * -cu: cutoff for ultra-paralog output (default: 50) - * -b: to use SDIse algorithm instead of GSDI algorithm (for binary species trees) ==== Gene tree ==== Must be in phyloXM format, with taxonomy and sequence data in appropriate fields ([http://forester.googlecode.com/files/wnt_gene_tree.xml example]). -- 1.7.10.2