--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ete_genetree_splitter.py	Mon Mar 12 12:51:48 2018 -0400
@@ -0,0 +1,56 @@
+from __future__ import print_function
+
+import optparse
+
+from ete3 import PhyloTree
+
+
+def main():
+    usage = "usage: %prog --genetree <genetree-file> --speciestree <speciestree-file> [options]"
+    parser = optparse.OptionParser(usage=usage)
+    parser.add_option('--genetree', help='GeneTree in nhx format')
+    parser.add_option('--speciestree', help='Species Tree in nhx format')
+    parser.add_option('--species_format', type='int', default=8, help='Species Tree input format (0-9)')
+    parser.add_option('--gene_node', type='int', default=0, help='Gene node format 0=gene_species, 1=species_gene')
+    parser.add_option('--gainlose', action='store_true', default=False, help='Find out gene gain/lose')
+    parser.add_option('--output_format', type='int', default=9, help='GeneTree output format (0-9)')
+    options, args = parser.parse_args()
+
+    if options.genetree is None:
+        parser.error("--genetree option must be specified, GeneTree in nhx format")
+
+    # reads single gene tree
+    genetree = PhyloTree(options.genetree)
+
+    # sets species naming function
+    if options.gene_node == 0:
+        genetree.set_species_naming_function(parse_sp_name)
+
+    # reconcile species tree with gene tree to help find out gene gain/lose
+    if options.gainlose:
+
+        if options.speciestree is None:
+            parser.error("--speciestree option must be specified, species tree in nhx format")
+
+        # reads species tree
+        speciestree = PhyloTree(options.speciestree, format=options.species_format)
+
+        # Removes '*' from Species names comes from Species tree configrured for TreeBest
+        for leaf in speciestree:
+            leaf.name = leaf.name.strip('*')
+
+        genetree, events = genetree.reconcile(speciestree)
+
+    # splits tree by duplication events which returns the list of all subtrees resulting from splitting current tree by its duplication nodes.
+    for cluster_id, node in enumerate(genetree.split_by_dups(), 1):
+        outfile = str(cluster_id) + '_genetree.nhx'
+        with open(outfile, 'w') as f:
+            f.write(node.write(format=options.output_format))
+
+
+def parse_sp_name(node_name):
+    return node_name.split("_")[1]
+
+
+if __name__ == "__main__":
+    main()