From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 29 Jun 2012 19:16:00 +0000 (+0000)
Subject: Edited wiki page GSDI through web user interface.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9fb521efd69ca1bbb41f8c64ea5e96929e05f996;p=jalview.git

Edited wiki page GSDI through web user interface.
---

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] <gene tree in phyloXML format> <species tree> [outfile]
+path/to/forester.jar org.forester.application.gsdi [-options] <gene tree in phyloXML format> <species tree> <outfile>
 }}}
 
 === 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)