From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 20 Dec 2012 01:17:02 +0000 (+0000)
Subject: Edited wiki page RIO through web user interface.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a91cc0e3a2cf93012e12b30f6716a0ec3f64f74d;p=jalview.git

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

diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki
index eb368e6..acc4a22 100644
--- a/wiki/RIO.wiki
+++ b/wiki/RIO.wiki
@@ -13,8 +13,8 @@ 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)
+  * `-f=<first>` : first gene tree to analyze (0-based index) (default: analyze all gene trees)
+  * `-l=<last>` : last gene tree to analyze (0-based index) (default: analyze all gene trees)
   * `-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)