From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 29 Jun 2012 19:21:03 +0000 (+0000)
Subject: Edited wiki page GSDI through web user interface.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fd9700636207a3d623be36e18a81f4be3b71baf7;p=jalview.git

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

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index 20fb526..c3673aa 100644
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -15,16 +15,21 @@ path/to/forester.jar org.forester.application.gsdi [-options] <gene tree in phyl
 === Options ===
 
   * -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)
-
-==== Species tree ====
-In phyloXML format (unless option -q is used), with taxonomy data in appropriate fields. Must be rooted, polytomies are allowed.
+ 
+  * -m: use most parimonious duplication model for GSDI:
+     assign nodes as speciations which would otherwise be assiged
+     as potential duplications due tp polytomies in the species tree
+  * -q: to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)
+  * -b: to use SDIse algorithm instead of GSDI algorithm (for binary species trees)
 
 ==== Gene tree ====
-In phyloXML format, with taxonomy and sequence data in appropriate fields. Must be rooted an binary (no polytomies).
+Must be in phyloXM format, with taxonomy and sequence data in appropriate fields.
 
+==== Species tree ====
+Must be in phyloXML format unless option -q is used.
+
+=== Options ===
+gsdi -g gene_tree.xml tree_of_life.xml out.xml
 
 == Description ==