fixing vector size issue...

[jalview.git] / wiki / GSDI.wiki

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index 2d6c3ae..4bd8a25 100644 (file)
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -1,41 +1,3 @@
 #summary generalized speciation duplication inference
 
-= Generalized Speciation Duplication Inference =
-
-== Purpose ==
-
-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]
-}}}
-
-=== 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)
-
-==== Species tree ====
-In phyloXML format (unless option -q is used), with taxonomy data in appropriate fields. Must be rooted, polytomies are allowed.
-
-==== Gene tree ====
-In phyloXML format, with taxonomy and sequence data in appropriate fields. Must be rooted an binary (no polytomies).
-
-
-== Description ==
-
-Currently, GSDI strips the gene tree of nodes for which a matching species is not present in the species tree. 
-
-== Reference ==
-
-Zmasek CM and Eddy SR "A simple algorithm to infer gene duplication and speciation events on a gene tree" [http://bioinformatics.oxfordjournals.org/content/17/9/821.abstract Bioinformatics, 17, 821-828]
- 
-
-
-== Download ==
-
-Download forester.jar here: http://code.google.com/p/forester/downloads/list
\ No newline at end of file
+https://sites.google.com/site/cmzmasek/home/software/forester/gsdi
\ No newline at end of file