1 = Gene tree Preprocessing =
5 Use EBI database to add species information to a gene tree which has sequence identifiers as labels.
10 path/to/forester.jar org.forester.application.gene_tree_preprocess <input tree in NH, NHX, Nexus, or phyloXML>
18 * input-name_preprocessed_gene_tree.phylo.xml
19 * input-name_removed_nodes.txt
24 Download forester.jar here: http://code.google.com/p/forester/downloads/list