From: cmzmasek@gmail.com Date: Wed, 28 Nov 2012 23:17:16 +0000 (+0000) Subject: Edited wiki page RIO through web user interface. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5723e1952c9a9532efbd626843d06dd53e2de83e;p=jalview.git Edited wiki page RIO through web user interface. --- diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki index c9b71af..578c2f8 100644 --- a/wiki/RIO.wiki +++ b/wiki/RIO.wiki @@ -32,10 +32,10 @@ path/to/forester.jar org.forester.application.rio [options] orthologies ==== Gene trees ==== -The gene trees ideally are in phyloXML,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"). +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 phyloXML format ([http://forester.googlecode.com/files/species.xml example]). +Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species.xml example]). === Examples === @@ -56,6 +56,8 @@ Must be in phyloXML format ([http://forester.googlecode.com/files/species.xml e 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 ==