X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FGSDI.wiki;h=ac4db98a08c33c77f229a54db9d7c12d9bb62511;hb=f6d7dfa06e34eaf7cc773cf7484e7b641296d452;hp=a5123003c1bd38ba95b71b323f07951c3108a57b;hpb=e444291943fc3eac8c7278416fddc0c6fe110cc7;p=jalview.git

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index a512300..ac4db98 100644
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -22,15 +22,15 @@ path/to/forester.jar org.forester.application.gsdi [-options] <gene tree in phyl
   * -b: to use SDIse algorithm instead of GSDI algorithm (for binary species trees)
 
 ==== Gene tree ====
-Must be in phyloXM format, with taxonomy and sequence data in appropriate fields.
+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"`.
 
@@ -48,9 +48,9 @@ GSDI can establish a taxonomic mapping between gene and species tree on the foll
 
 
 === 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)]
+  * [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 ==