From 9fb521efd69ca1bbb41f8c64ea5e96929e05f996 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 29 Jun 2012 19:16:00 +0000 Subject: [PATCH] Edited wiki page GSDI through web user interface. --- wiki/GSDI.wiki | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki index 2d6c3ae..20fb526 100644 --- a/wiki/GSDI.wiki +++ b/wiki/GSDI.wiki @@ -9,12 +9,12 @@ To infer duplication events on a gene tree given a trusted species tree. == Usage == {{{ java -Xmx1024m -cp -path/to/forester.jar org.forester.application.gsdi [-options] [outfile] +path/to/forester.jar org.forester.application.gsdi [-options] }}} === Options === - * -s: to strip the species tree prior to duplication inference + * -g: to allow stripping of gene tree nodes without a matching species in the species tree * -b: to use SDI algorithm instead of GSDI algorithm * -m: use most parimonious duplication model for GSDI: assign nodes as speciations which would otherwise be assiged as unknown because of polytomies in the species tree * -q: to allow species tree in other formats than phyloXML (Newick, NHX, Nexus) -- 1.7.10.2