inprogress

[jalview.git] / wiki / GSDI.wiki

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index e0c1007..ac4db98 100644 (file)
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -25,12 +25,12 @@ path/to/forester.jar org.forester.application.gsdi [-options] <gene tree in phyl
 Must be in phyloXM format, with taxonomy and sequence data in appropriate fields ([http://forester.googlecode.com/files/wnt_gene_tree.xml example]).
 
 ==== Species tree ====
-Must be in phyloXML format unless option -q is used.
+Must be in phyloXML format unless option -q is used ([http://forester.googlecode.com/files/species.xml example]).
 
 === 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 log file, ending in `"_gsdi_log.txt"` ([http://forester.googlecode.com/files/wnt_gsdi_log.txt example])
   * 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"`.