X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FGSDI.wiki;h=19b63fc8da930b64ede12b1ff29bde81077786a0;hb=39abf0d16f644fce23e01cc638bb64518e3b9152;hp=f662060f6c270ae5408b671c3d82607291023975;hpb=cc7802c62f2b4997dd8eefbabd244e1b36b0ee13;p=jalview.git

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index f662060..19b63fc 100644
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -7,10 +7,9 @@
 To infer duplication events on a gene tree given a trusted species tree.
 
 == Usage == 
-{{{
-java -Xmx1024m -cp
-path/to/forester.jar org.forester.application.gsdi [-options] <gene tree in phyloXML format> <species tree> <outfile>
-}}}
+
+`java -Xmx1024m -cp
+path/to/forester.jar org.forester.application.gsdi [-options] <gene tree in phyloXML format> <species tree> <outfile>`
 
 === Options ===
 
@@ -29,12 +28,12 @@ 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 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'.
+  * 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
+`gsdi -g gene_tree.xml tree_of_life.xml out.xml`