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[jalview.git] / wiki / genetreepreprocessing.wiki

diff --git a/wiki/genetreepreprocessing.wiki b/wiki/genetreepreprocessing.wiki
index d2d951c..25348f9 100644 (file)
--- 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
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+  * 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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