From 7b7c486ecdf0b1ac0c0d1f088636bd0b7b4d4a3f Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Sat, 24 May 2014 00:11:34 +0000 Subject: [PATCH] Edited wiki page GSDI through web user interface. --- wiki/GSDI.wiki | 63 +------------------------------------------------------- 1 file changed, 1 insertion(+), 62 deletions(-) diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki index ac4db98..4bd8a25 100644 --- a/wiki/GSDI.wiki +++ b/wiki/GSDI.wiki @@ -1,64 +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 ([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 \ No newline at end of file +https://sites.google.com/site/cmzmasek/home/software/forester/gsdi \ No newline at end of file -- 1.7.10.2