X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FGSDI.wiki;h=a5123003c1bd38ba95b71b323f07951c3108a57b;hb=e444291943fc3eac8c7278416fddc0c6fe110cc7;hp=8c611d8b697212e2db5c83ec2e08b8bf038bc49a;hpb=4d2e922a9ebe8e69499d2470f6468b2d8b3d7454;p=jalview.git

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index 8c611d8..a512300 100644
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -32,11 +32,25 @@ Must be in phyloXML format unless option -q is used.
 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"`.
+  * 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.xml out.xml`
+`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 ==