From: cmzmasek@gmail.com Date: Wed, 28 Nov 2012 23:19:29 +0000 (+0000) Subject: Edited wiki page RIO through web user interface. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9c1299acd081df2bd8c6c7320ce7f102f0fa5440;p=jalview.git Edited wiki page RIO through web user interface. --- diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki index 578c2f8..954f6e3 100644 --- a/wiki/RIO.wiki +++ b/wiki/RIO.wiki @@ -32,7 +32,7 @@ path/to/forester.jar org.forester.application.rio [options] orthologies ==== 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"). +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 [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species.xml example]).