X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FPhyloBioRuby.wiki;h=06d577721e3e5c0ab8386b1733bf51b42297de4a;hb=211364763c73cc916843e5df5d1412d14a57359e;hp=204edf0e545515625042894a739762a14b64584e;hpb=8ace8ed9c6cf72b4e3bfd613f2224c8d201ea040;p=jalview.git

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index 204edf0..06d5777 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -13,14 +13,21 @@ Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby --
 
 == Calculating a Multiple Sequence Alignment  ==
 
+BioRuby can be used to execute a variety of multiple sequence alignment
+programs (such as MAFFT, Probcons, ClustalW, Muscle). 
+In the following, examples for using the MAFFT and 
+
 === MAFFT ===
 
+
+
 {{{
 #!/usr/bin/env ruby
 require 'bio'
 
-# Calculates the alignment using the MAFFT program
-# on the local machine, and stores the result in 'report'.
+# 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)
@@ -33,6 +40,27 @@ 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 }
+#
+}}}
+
 
 
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