X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=wiki%2Fgenetreepreprocessing.wiki;h=25348f9535efca4f298422d8e1172b9f06a3df39;hb=97358f7a982d67831aedc14d5ab193727f6bdc83;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 `
+{{{
+java -Xmx1024m -cp
+path/to/forester.jar org.forester.application.gene_tree_preprocess
+}}}
== Details ==
-Output is two files:
- * _preprocessed_gene_tree.phylo.xml
- * _removed_nodes.txt
\ No newline at end of file
+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
\ No newline at end of file