#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

{{{
#!/usr/bin/env ruby
require 'bio'

}}}


== 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], [http://probcons.stanford.edu/ Probcons], [http://www.clustal.org/ ClustalW], [http://www.drive5.com/muscle/ 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 }
#
}}}


== Manipulating Multiple Sequence Alignment  ==

It is probably a good idea to 'clean up' multiple sequence to be used
for phylogenetic inference. For instance, columns with more than 50% gaps can be deleted, like so:


... to be done

{{{
#!/usr/bin/env ruby
require 'bio'

}}}


= Phylogenetic Inference =

== Maximum Likelihood ==

=== RAxML ===

... to be done

{{{
#!/usr/bin/env ruby
require 'bio'

}}}


== Pairwise Distance Based Methods ==

=== FastME ===

... to be done

{{{
#!/usr/bin/env ruby
require 'bio'

}}}