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[jalview.git] / wiki / GSDI.wiki

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 #summary generalized speciation duplication inference
 
-= 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)
-
-==== Species tree ====
-In phyloXML format (unless option -q is used), with taxonomy data in appropriate fields. Must be rooted, polytomies are allowed.
-
-==== Gene tree ====
-In phyloXM format, with taxonomy and sequence data in appropriate fields. Must be rooted an binary (no polytomies).
-
-
-
-== Download ==
-
-Download forester.jar here: http://code.google.com/p/forester/downloads/list
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+https://sites.google.com/site/cmzmasek/home/software/forester/gsdi
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