#summary preprocessing of gene trees for speciation/duplication inference

= Generalized Speciation Duplication Inference

== Purpose ==

Infer duplication events on a gene tree given a trusted species tree.

== Usage == 
{{{
java -Xmx1024m -cp
path/to/forester.jar org.forester.application.gene_tree_preprocess <input tree in NH, NHX, Nexus, or phyloXML>
}}}



== 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