-#Gene tree preprocessing
+#summary preprocessing of gene trees for speciation/duplication inference
-= Introduction =
+= Gene tree preprocessing =
-Add your content here.
+== Purpose ==
+Use EBI database to add species information to a gene tree which has sequence identifiers as labels.
-= Details =
+== Usage ==
+{{{
+java -Xmx1024m -cp
+path/to/forester.jar org.forester.application.gene_tree_preprocess <input tree in NH, NHX, Nexus, or phyloXML>
+}}}
-Add your content here. Format your content with:
- * Text in *bold* or _italic_
- * Headings, paragraphs, and lists
- * Automatic links to other wiki pages
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+
+
+== Details ==
+
+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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