From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 24 Feb 2011 07:50:14 +0000 (+0000)
Subject: Edited wiki page PhyloBioRuby through web user interface.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fbc08ff6b8d8d5f72cf36dbb600c891ffa6d8c2b;p=jalview.git

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

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index e05a191..84ef1e9 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -9,7 +9,22 @@ Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby --
 
 == Reading in a Multiple Sequence Alignment from a File ==
 
-== Calculating a Multiple Sequence Alignment  =
+... to be done
+
+== Calculating a Multiple Sequence Alignment  ==
+
+=== MAFFT ===
+
+'
+#!/usr/bin/env ruby
+require 'bio'
+options = [ '--maxiterate', '1000', '--localpair' ]
+mafft = Bio::MAFFT.new('/home/zma/SOFTWARE/mafft-6.847-without-extensions/scripts/mafft', options )
+report = mafft.query_align( seqs)
+'
+
+
+
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