#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 =


== Multiple Sequence Alignment Input and Output ==

=== Reading in a Multiple Sequence Alignment 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], and [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html T-Coffee]). 
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.
align.each { |s| puts s.to_s }

}}}

References:

 * Katoh, Toh (2008) "Recent developments in the MAFFT multiple sequence alignment program" Briefings in Bioinformatics 9:286-298 

 * Katoh, Toh 2010 (2010) "Parallelization of the MAFFT multiple sequence alignment program" Bioinformatics 26:1899-1900 



=== 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.
align.each { |s| puts s.to_s }

}}}

References:

 * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797

=== Other Programs ===

[http://probcons.stanford.edu/ Probcons], [http://www.clustal.org/ ClustalW], and [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html T-Coffee]) can be used in the same manner as the programs above. 


== 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 =

== Phylogenetic Tree Input and Output ==

=== Reading in of Phylogenetic Trees ===

_... to be done_

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

}}}

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



=== 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 wrappers for phylogenetic inference programs, thus I am progress of writing a RAxML wrapper followed by a wrapper for FastME..._

_What about pairwise distance calculation?_



== Maximum Likelihood ==

=== RAxML ===

_... to be done_

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

}}}


=== PhyML ===

_... to be done_

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

}}}

== Pairwise Distance Based Methods ==

=== FastME ===

_... to be done_

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

}}}



=== PHYLIP? ===



== Support Calculation? ==

=== Bootstrap Resampling? ===


----

= Analyzing Phylogenetic Trees =

== PAML ==


== Gene Duplication Inference ==

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


== Others? ==