From 8cd220e1ba16d9d1a180aa8174695b397efb97e0 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 29 Nov 2012 21:46:48 +0000 Subject: [PATCH] Edited wiki page RIO through web user interface. --- wiki/RIO.wiki | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki index 0293adf..70756ef 100644 --- a/wiki/RIO.wiki +++ b/wiki/RIO.wiki @@ -26,8 +26,7 @@ java -Xmx2048m -cp forester.jar org.forester.application.rio [options] `and/or output for -one query sequence with -q and a `[`outfile`]` are required. +Either output of all vs. all ortholgy support with -t=`<`output table`>` and/or output for one query sequence with -q and a `[`outfile`]` are required. ==== Sort ==== @@ -48,12 +47,11 @@ Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([ht `rio gene_trees.nh species.xml -t=outtable` - === Example files === - * [http://forester.googlecode.com/files/wnt_gene_tree.xml gene tree] - * [http://forester.googlecode.com/files/species.xml species tree] - * [http://forester.googlecode.com/files/wnt_gsdi_log.txt log file (output)] - + * [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"] + == References == -- 1.7.10.2