From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 29 Jun 2012 19:36:41 +0000 (+0000)
Subject: Edited wiki page GSDI through web user interface.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4d2e922a9ebe8e69499d2470f6468b2d8b3d7454;p=jalview.git

Edited wiki page GSDI through web user interface.
---

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index e2559f6..8c611d8 100644
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -16,7 +16,9 @@ path/to/forester.jar org.forester.application.gsdi [-options] <gene tree in phyl
   * -g: to allow stripping of gene tree nodes without a matching species in the species tree
  
   * -m: use most parimonious duplication model for GSDI: assign nodes as speciations which would otherwise be assiged as potential duplications due tp polytomies in the species tree
+
   * -q: to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)
+
   * -b: to use SDIse algorithm instead of GSDI algorithm (for binary species trees)
 
 ==== Gene tree ====
@@ -33,7 +35,7 @@ Besides the main output of a gene tree with duplications and speciations assigne
   * 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 -q gene_tree.xml tree_of_life.xml out.xml`