X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FPhyloBioRuby.wiki;h=6294fbe6a163c53e4454579800d446f456365f1c;hb=1693a5a129dcb4b292dd4dd6bda1159217c5a510;hp=9c85ae262a42f6136e4ccef2a82b6e8bf9bf8d49;hpb=4b77bc0f300b6bab56794a7967a50d40603f38e4;p=jalview.git

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index 9c85ae2..6294fbe 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -1,11 +1,67 @@
-#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  ==
+
+BioRuby can be used to execute a variety of multiple sequence alignment
+programs (such as [http://mafft.cbrc.jp/alignment/software/ MAFFT], Probcons, ClustalW, Muscle). 
+In the following, examples for using the MAFFT and Muscle are shown.
+
+=== MAFFT ===
+
+
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+# Calculates the alignment using the MAFFT program on the local
+# machine with options '--maxiterate 1000 --localpair'
+# and stores the result in 'report'.
+options = [ '--maxiterate', '1000', '--localpair' ]
+mafft = Bio::MAFFT.new('path/to/mafft', options )
+report = mafft.query_align( seqs)
+
+# Accesses the actual alignment
+align = report.alignment
+
+# Prints each sequence to the console.
+report.align.each { |s| puts s.to_s }
+#
+}}}
+
+=== Muscle ===
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+# Calculates the alignment using the Muscle program on the local
+# machine with options '-quiet -maxiters 64'
+# and stores the result in 'report'.
+options = [ '-quiet', '-maxiters', '64' ]
+muscle = Bio::Muscle.new('path/to/muscle', options )
+report = muscle.query_align( seqs)
+
+# Accesses the actual alignment
+align = report.alignment
+
+# Prints each sequence to the console.
+report.align.each { |s| puts s.to_s }
+#
+}}}
 
 
-= Details =
 
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