fixing vector size issue...

[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 ===
-
-  * -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 bases 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 gene_tree.xml tree_of_life.xml 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
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+https://sites.google.com/site/cmzmasek/home/software/forester/gsdi
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