Edited wiki page GSDI through web user interface.

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index 928dbce..0f57750 100644 (file)
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -27,6 +27,13 @@ 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.
 
+=== 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 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:
@@ -34,12 +41,7 @@ GSDI can establish a taxonomic mapping between gene and species tree on the foll
   * 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 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 -q gene_tree.xml tree_of_life.nwk out.xml`