X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FGSDI.wiki;h=4bd8a2545a82e679d41bc006d951e5ba394698f3;hb=3028159552c6c5946ca2a0cba56c03ba32146551;hp=13c8c4e30358d4cc8a8aea87f997aceb6b5bbe33;hpb=cd50bc9bab17eb4e3837ab40ec3a7e9fdf202714;p=jalview.git diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki index 13c8c4e..4bd8a25 100644 --- a/wiki/GSDI.wiki +++ b/wiki/GSDI.wiki @@ -1,44 +1,3 @@ #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] -}}} - -=== Options === - - * -g: to allow stripping of gene tree nodes without a matching species in the species tree - - * -m: use most parimonious duplication model for GSDI: assign nodes as speciations which would otherwise be assiged as potential duplications due tp polytomies in the species tree - * -q: to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus) - * -b: to use SDIse algorithm instead of GSDI algorithm (for binary species trees) - -==== Gene tree ==== -Must be in phyloXM format, with taxonomy and sequence data in appropriate fields. - -==== Species tree ==== -Must be in phyloXML format unless option -q is used. - -=== Options === -gsdi -g gene_tree.xml tree_of_life.xml out.xml - -== Description == - -Currently, GSDI strips the gene tree of nodes for which a matching species is not present in the species tree. - -== Reference == - -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] - - - -== Download == - -Download forester.jar here: http://code.google.com/p/forester/downloads/list \ No newline at end of file +https://sites.google.com/site/cmzmasek/home/software/forester/gsdi \ No newline at end of file