-= 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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