X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2Fgenetreepreprocessing.wiki;h=25348f9535efca4f298422d8e1172b9f06a3df39;hb=886c0c0a7a7cef72503df9f21762db1dab594362;hp=4c365a4715c1be882b4345f53abcf5e2b41ecec1;hpb=f65497d6d09c77f37b9371f164e988276a44b1bd;p=jalview.git

diff --git a/wiki/genetreepreprocessing.wiki b/wiki/genetreepreprocessing.wiki
index 4c365a4..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:
-  * <input>_preprocessed_gene_tree.phylo.xml
-  * <input>_removed_nodes.txt
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+Output consists of three files:
+  * input-name_preprocessed_gene_tree.phylo.xml
+  * input-name_species_present.txt
+  * input-name_removed_nodes.txt
+
+
+== Download ==
+
+Download forester.jar here: http://code.google.com/p/forester/downloads/list
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