From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 20 Dec 2012 01:16:12 +0000 (+0000)
Subject: Edited wiki page RIO through web user interface.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5a655d5fbaaac8857f9c19a6ba375f76a5f894d5;p=jalview.git

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

diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki
index a10b4eb..eb368e6 100644
--- a/wiki/RIO.wiki
+++ b/wiki/RIO.wiki
@@ -15,9 +15,9 @@ java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene tre
 === Options ===
   * `-f=<first>` : first gene tree to analyze (0-based index)
   * `-l=<last>` : last gene tree to analyze (0-based index)
-  * -r=<re-rooting> : re-rooting method for gene trees, possible values or 'none', 'midpoint', or 'outgroup' (default: by minizming duplications)
-  * -o=<outgroup>  : for rooting by outgroup, name of outgroup (external gene tree node)
-  * -b : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed) 
+  * `-r=<re-rooting>` : re-rooting method for gene trees, possible values or 'none', 'midpoint', or 'outgroup' (default: by minizming duplications)
+  * `-o=<outgroup>` : for rooting by outgroup, name of outgroup (external gene tree node)
+  * `-b` : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed) 
 
   
 ==== Gene trees ====