X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2Fgenetreepreprocessing.wiki;h=25348f9535efca4f298422d8e1172b9f06a3df39;hb=b6366fd2ac865514d2ceacb63432dac532147a85;hp=d2d951c4b92f1daf54e855b63563c27b73db2394;hpb=04527e08a3624086d15e36047ec73f054d8da977;p=jalview.git

diff --git a/wiki/genetreepreprocessing.wiki b/wiki/genetreepreprocessing.wiki
index d2d951c..25348f9 100644
--- a/wiki/genetreepreprocessing.wiki
+++ b/wiki/genetreepreprocessing.wiki
@@ -1,13 +1,27 @@
-= Gene tree Preprocessing =
+#summary preprocessing of gene trees for speciation/duplication inference
+
+= Gene tree preprocessing =
+
+== Purpose ==
+
+Use EBI database to add species information to a gene tree which has sequence identifiers as labels.
 
 == Usage == 
-{{{java -Xmx1024m -cp
-path/to/forester.jar org.forester.application.gene_tree_preprocess <input tree in NH, NHX, Nexus, or phyloXML>}}}
+{{{
+java -Xmx1024m -cp
+path/to/forester.jar org.forester.application.gene_tree_preprocess <input tree in NH, NHX, Nexus, or phyloXML>
+}}}
 
 
 
 == Details ==
 
-Output is two files:
+Output consists of three files:
   * input-name_preprocessed_gene_tree.phylo.xml
-  * input-name_removed_nodes.txt
\ No newline at end of file
+  * input-name_species_present.txt
+  * input-name_removed_nodes.txt
+
+
+== Download ==
+
+Download forester.jar here: http://code.google.com/p/forester/downloads/list
\ No newline at end of file