#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 ([http://forester.googlecode.com/files/wnt_gene_tree.xml example]).

==== Species tree ====
Must be in phyloXML format unless option -q is used ([http://forester.googlecode.com/files/species.xml example]).

=== 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"` ([http://forester.googlecode.com/files/wnt_gsdi_log.txt example])
  * 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"`.

=== Taxonomic mapping between gene and species tree ===

GSDI can establish a taxonomic mapping between gene and species tree on the following three data fields:
  * scientific names (e.g. "Pyrococcus horikoshii")
  * taxonomic identifiers (e.g. "35932" from uniprot or ncbi)
  * taxonomy codes (e.g. "PYRHO") 



=== Example ===
`gsdi -g -q gene_tree.xml tree_of_life.nwk out.xml`


=== Example files ===
  * [http://forester.googlecode.com/files/wnt_gene_tree.xml gene tree]
  * [http://forester.googlecode.com/files/species.xml species tree]
  * [http://forester.googlecode.com/files/wnt_gsdi_log.txt log file (output)]


== 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