#!/usr/bin/env ruby
require 'bio'
-# Calculates the alignment using the MAFFT program
-# on the local machine with options
-# '--maxiterate', '1000', '--localpair'
+# 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 )
=== Muscle ===
-<ruby>
+{{{
#!/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 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)
# Prints each sequence to the console.
report.align.each { |s| puts s.to_s }
#
-</ruby>
+}}}
+
+
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