Edited wiki page GSDI through web user interface.

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index 13c8c4e..27b1b7b 100644 (file)
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -26,12 +26,17 @@ 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.
 
-=== Options ===
+=== 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
 
-== Description ==
 
-Currently, GSDI strips the gene tree of nodes for which a matching species is not present in the species tree. 
 
 == Reference ==