#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 Alignments from a File ==

_... to be done_

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

}}}


== Writing a Multiple Sequence Alignment to a File ==

_... to be done_

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

}}}



== Calculating Multiple Sequence Alignments  ==

!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 Alignments ==

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 Trees =

== Reading and Writing of Phylogenetic Trees ==

_... to be done_

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

}}}

Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation


== Phylogenetic Inference ==

*Currently !BioRuby does not contain any wrappers for phylogenetic inference, I am progress of writing a RAxML wrapper followed by a wrapper for FastMA.*

== 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'

}}}


= Analyzing Phylogenetic Trees =

== Gene Duplication Inference ==

_need to further test and then import GSoC 'SDI' work..._


== Others? ==