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 phyloXML format, with taxonomy and sequence data in appropriate fields. Must be rooted an binary (no polytomies).
31 Currently, GSDI strips the gene tree of nodes for which a matching species is not present in the species tree.
35 Zmasek CM and Eddy SR "A simple algorithm to infer gene duplication and speciation events on a gene tree" [http://bioinformatics.oxfordjournals.org/content/17/9/821.abstract Bioinformatics, 17, 821-828]
41 Download forester.jar here: http://code.google.com/p/forester/downloads/list