From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 8 Jun 2012 14:27:46 +0000 (+0000)
Subject: Edited wiki page GSDI through web user interface.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5f48fe3c95108893b0f52659170b7074256091a6;p=jalview.git

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

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index a875f25..4956a5b 100644
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -1,17 +1,27 @@
-#summary preprocessing of gene trees for speciation/duplication inference
+#summary generalized speciation duplication inference
 
 = Generalized Speciation Duplication Inference
 
 == Purpose ==
 
-Infer duplication events on a gene tree given a trusted species tree.
+To infer duplication events on a gene tree given a trusted species tree.
 
 == Usage == 
 {{{
 java -Xmx1024m -cp
-path/to/forester.jar org.forester.application.gene_tree_preprocess <input tree in NH, NHX, Nexus, or phyloXML>
+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
+ *  -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)
+
 
 
 == Details ==