X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FGSDI.wiki;h=c5eb5e63754e18e2eee7ad8159714ac9ae2b83c1;hb=d89babefe5728a059761b9053f90d0adadf66dd7;hp=bcb6849d661c8257e963ec7e54f1e9085f27f0a2;hpb=f31f530a515e0856df35eccbf1f18cddb8697952;p=jalview.git

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index bcb6849..c5eb5e6 100644
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -7,24 +7,40 @@
 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.
 
 ==== Species tree ====
-In phyloXML format (unless option -q is used), with taxonomy data in appropriate fields. Must be rooted, polytomies are allowed.
+Must be in phyloXML format unless option -q is used.
 
-==== Gene tree ====
-In phyloXM format, with taxonomy and sequence data in appropriate fields. Must be rooted an binary (no polytomies).
+=== 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 ==