1 #summary generalized speciation duplication inference
3 = Generalized Speciation Duplication Inference
7 To infer duplication events on a gene tree given a trusted species tree.
12 path/to/forester.jar org.forester.application.gsdi [-options] <gene tree in phyloXML format> <species tree> [outfile]
17 * -s: to strip the species tree prior to duplication inference
18 * -b: to use SDI algorithm instead of GSDI algorithm
19 * -m: use most parimonious duplication model for GSDI: assign nodes as speciations which would otherwise be assiged as unknown because of polytomies in the species tree
20 * -q: to allow species tree in other formats than phyloXML (Newick, NHX, Nexus)
26 Output consists of three files:
27 * input-name_preprocessed_gene_tree.phylo.xml
28 * input-name_species_present.txt
29 * input-name_removed_nodes.txt
34 Download forester.jar here: http://code.google.com/p/forester/downloads/list