X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FGSDI.wiki;h=928dbceefd58671a160e22f59b82f2ea9f456921;hb=d08c3ec6cb69dd9cf44d9dfcb45b3530ba608d92;hp=e2559f61f16d11112f7de23f598757e1649c95c0;hpb=12507a918ca187611aa4af2720d3b0191e0dbfe8;p=jalview.git

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index e2559f6..928dbce 100644
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -16,7 +16,9 @@ path/to/forester.jar org.forester.application.gsdi [-options] <gene tree in phyl
   * -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 ====
@@ -25,15 +27,22 @@ Must be in phyloXM format, with taxonomy and sequence data in appropriate fields
 ==== Species tree ====
 Must be in phyloXML format unless option -q is used.
 
+=== 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") 
+
 === 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"`.
+  * 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"`.
 
 === Example ===
-`gsdi -g gene_tree.xml tree_of_life.xml out.xml`
+`gsdi -g -q gene_tree.xml tree_of_life.nwk out.xml`