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 * -g: to allow stripping of gene tree nodes without a matching species in the species tree
19 * -m: use most parimonious duplication model for GSDI:
20 assign nodes as speciations which would otherwise be assiged
21 as potential duplications due tp polytomies in the species tree
22 * -q: to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)
23 * -b: to use SDIse algorithm instead of GSDI algorithm (for binary species trees)
26 Must be in phyloXM format, with taxonomy and sequence data in appropriate fields.
28 ==== Species tree ====
29 Must be in phyloXML format unless option -q is used.
32 gsdi -g gene_tree.xml tree_of_life.xml out.xml
36 Currently, GSDI strips the gene tree of nodes for which a matching species is not present in the species tree.
40 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]
46 Download forester.jar here: http://code.google.com/p/forester/downloads/list