From: cmzmasek@gmail.com Date: Wed, 28 Nov 2012 23:08:06 +0000 (+0000) Subject: Edited wiki page rio through web user interface. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=aff69eeffcce19d0912e9dd5ef727751098ffa8a;p=jalview.git Edited wiki page rio through web user interface. --- diff --git a/wiki/rio.wiki b/wiki/rio.wiki index 76a4ae7..180a553 100644 --- a/wiki/rio.wiki +++ b/wiki/rio.wiki @@ -27,15 +27,16 @@ path/to/forester.jar org.forester.application.rio [options] super orthologies - 2: super orthologies > orthologies + * 0: orthologies + * 1: orthologies > super orthologies + * 2: super orthologies > orthologies -==== 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]). +==== Gene trees ==== +The gene trees ideally are in phyloXML, 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 unless option -q is used ([http://forester.googlecode.com/files/species.xml example]). +Must be in phyloXML format ([http://forester.googlecode.com/files/species.xml example]). === Output ===