-= Generalized Speciation Duplication Inference
-
-== Purpose ==
-
-To infer duplication events on a gene tree given a trusted species tree.
-
-== Usage ==
-{{{
-java -Xmx1024m -cp
-path/to/forester.jar org.forester.application.gsdi [-options] <gene tree in phyloXML format> <species tree> [outfile]
-}}}
-
-=== Options ===
-
- *s : to strip the species tree prior to duplication inference
- * -b: to use SDI algorithm instead of GSDI algorithm
- * -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
- * -q: to allow species tree in other formats than
- phyloXML (Newick, NHX, Nexus)
-
-
-
-== 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
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