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)
22 ==== Species tree ====
23 In phyloXML format (unless option -q is used), with taxonomy data in appropriate fields. Must be rooted, polytomies are allowed.
26 In phyloXM format, with taxonomy and sequence data in appropriate fields. Must be rooted an binary (no polytomies).
32 Download forester.jar here: http://code.google.com/p/forester/downloads/list