X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FPhyloBioRuby.wiki;h=bfb1c4cbc822b8c032214b962c56010d616eeba9;hb=4fb2be47b1fcf014f2e3f327e69833a458b99c4d;hp=9c85ae262a42f6136e4ccef2a82b6e8bf9bf8d49;hpb=4b77bc0f300b6bab56794a7967a50d40603f38e4;p=jalview.git

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index 9c85ae2..bfb1c4c 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -1,11 +1,29 @@
-#summary Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby
+#summary Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!
 
 = Introduction =
 
-Add your content here.
+Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!.
+
+
+= Multiple Sequence Alignments =
+
+== Reading in a Multiple Sequence Alignment from a File ==
+
+... 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)
+}}}
 
 
-= Details =
 
 Add your content here.  Format your content with:
   * Text in *bold* or _italic_