X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FGSDI.wiki;h=4bd8a2545a82e679d41bc006d951e5ba394698f3;hb=6aabb22c6b134e4e1860e97f7994fec02b584906;hp=aeadf5d27fa606c4de2e79c4a6363bcf54288225;hpb=93595a2f1d11f5637022563cc475aff7d19eb9db;p=jalview.git diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki index aeadf5d..4bd8a25 100644 --- a/wiki/GSDI.wiki +++ b/wiki/GSDI.wiki @@ -1,50 +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. - -=== Output === - -Besides the main output of a gene tree with duplications and speciations assigned to all of its internal nodes, this program also produces the following: - * a log file, ending in `"_gsdi_log.txt"` - * a species tree file which only contains external nodes with were needed for the reconciliation, ending in `"_species_tree_used.xml"` - * if the gene tree contains species with scientific species names such as "Pyrococcus horikoshii strain ATCC 700860" and if a mapping cannot be establish based on these, GSDI will attempt to map by removing the "strain" (or "subspecies") information, these will be listed in a file ending in `"_gsdi_remapped.txt"`. - -=== Example === -`gsdi -g -q gene_tree.xml tree_of_life.nwk out.xml` - - - -== 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