#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  ==

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 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 ===

<ruby>
#!/usr/bin/env ruby
require 'bio'

# Calculates the alignment using the MAFFT program
# on the local machine, 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 }
#
</ruby>

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