X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FGSDI.wiki;h=ac4db98a08c33c77f229a54db9d7c12d9bb62511;hb=7bbb45295594e9574ee64a32fac17a93b5aa6ade;hp=93395b6a3afb3a845d86d2f045ed493229283d78;hpb=6229653c2e9cb57748f363a78c2cc42676db3e4b;p=jalview.git

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index 93395b6..ac4db98 100644
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -1,6 +1,6 @@
 #summary generalized speciation duplication inference
 
-= Generalized Speciation Duplication Inference
+= Generalized Speciation Duplication Inference =
 
 == Purpose ==
 
@@ -9,24 +9,54 @@ 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]
+path/to/forester.jar org.forester.application.gsdi [-options] <gene tree in phyloXML format> <species tree> <outfile>
 }}}
-
 === Options ===
 
-  * -s: to strip the species tree prior to duplication inference
-  * -b: to use SDI algorithm instead of GSDI algorithm
-  * -m: use most parimonious duplication model for GSDI: assign nodes as speciations which would otherwise be assiged as unknown because of polytomies in the species tree
-  * -q: to allow species tree in other formats than phyloXML (Newick, NHX, Nexus)
+  * -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)]
 
 
-== Details ==
+== Reference ==
 
-Output consists of three files:
-  * input-name_preprocessed_gene_tree.phylo.xml
-  * input-name_species_present.txt
-  * input-name_removed_nodes.txt
+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 ==