Edited wiki page GSDI through web user interface.

[jalview.git] / wiki / GSDI.wiki

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index 4d83100..19b63fc 100644 (file)
--- 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 ===
 
@@ -30,11 +29,11 @@ Must be in phyloXML format unless option -q is used.
 
 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 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`