From: cmzmasek@gmail.com Date: Thu, 29 Nov 2012 21:49:27 +0000 (+0000) Subject: Edited wiki page RIO through web user interface. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=12dcbed140836c15a8294e2b575f72d86909bbd5;p=jalview.git Edited wiki page RIO through web user interface. --- diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki index 70756ef..144d2f1 100644 --- a/wiki/RIO.wiki +++ b/wiki/RIO.wiki @@ -35,13 +35,15 @@ Either output of all vs. all ortholgy support with -t=`<`output table`>` and/or * 2: super orthologies > 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") ([http://forester.googlecode.com/files/gene_trees_rio.nh example]). ==== Species tree ==== -Must be in [http://www.biomedcentral.com/1471-2105/10/356/ 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_tree_rio.xml example]). === Examples === +`rio gene_trees_rio.nh species_tree_rio.xml outfile -q=D_HUMAN -t=outtable -u -cu=10 -co=10` + `rio gene_trees.nh species.xml outfile -q=BCL2_HUMAN -t=outtable -u -cu=60 -co=60` `rio gene_trees.nh species.xml -t=outtable` @@ -50,7 +52,7 @@ Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([ht === Example files === * [http://forester.googlecode.com/files/gene_trees_rio.nh gene trees file] * [http://forester.googlecode.com/files/species_tree_rio.xml species tree file] - * [http://forester.googlecode.com/files/rio_outfile.txt output, for query "D_HUMAN"] + * [http://forester.googlecode.com/files/rio_outfile.txt output] (for query "D_HUMAN") == References ==