X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FGSDI.wiki;h=0f57750e4bb89f044b7cded37afe2b954a818d2c;hb=dd976779b8df8db52359fe458b4ccccd94bdc52a;hp=27b1b7b4928369489d35085d9b35ed21dac72058;hpb=49bc4d0b1bdd4d10210d2c59b800c8133d045cab;p=jalview.git

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index 27b1b7b..0f57750 100644
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -11,13 +11,14 @@ To infer duplication events on a gene tree given a trusted species tree.
 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 ====
@@ -29,12 +30,21 @@ 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".
+  * 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 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 gene_tree.xml tree_of_life.xml out.xml
+`gsdi -g -q gene_tree.xml tree_of_life.nwk out.xml`