#summary Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!

= Introduction =

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)
'



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