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



= Introduction =

Under development!

Tutorial for multiple sequence alignments and phylogenetic methods in [http://bioruby.open-bio.org/ BioRuby].

Eventually, this is expected to be placed on the official !BioRuby page.

Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute

 
Copyright (C) 2011 Christian M Zmasek


= Multiple Sequence Alignments =


== Multiple Sequence Alignment Input and Output ==

=== Reading in a Multiple Sequence Alignment from a File ===

The following example shows how to read in a *ClustalW*-formatted multiple sequence alignment.

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

# Reads in a ClustalW-formatted multiple sequence alignment
# from a file named "infile_clustalw.aln" and stores it in 'report'.
report = Bio::ClustalW::Report.new(File.read('infile_clustalw.aln'))

# Accesses the actual alignment.
msa = report.alignment

# Goes through all sequences in 'msa' and prints the
# actual molecular sequence.
msa.each do |entry|
  puts entry.seq
end
}}}

 

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


The following example shows how to write a multiple sequence alignment in *FASTA*-format. It first creates a file named "outfile.fasta" for writing ('w') and then writes the multiple sequence alignment referred to by variable 'msa' to it in FASTA-format (':fasta').

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

# Creates a new file named "outfile.fasta" and writes
# multiple sequence alignment 'msa' to it in fasta format.
File.open('outfile.fasta', 'w') do |f|
  f.write(msa.output(:fasta))
end
}}}

==== Setting the Output Format ====

The following constants determine the output format.

  * ClustalW: `:clustal`
  * FASTA:    `:fasta`
  * PHYLIP interleaved (will truncate sequence names to no more than 10 characters): `:phylip`
  * PHYLIP non-interleaved (will truncate sequence names to no more than 10 characters): `:phylipnon`
  * MSF: `:msf`
  * Molphy: `:molphy`


For example, the following writes PHYLIP's non-interleaved format:

{{{
f.write(align.output(:phylipnon))
}}}


== Formatting of Individual Sequences ==

_... to be done_

!BioRuby can format molecular sequences in a variety of formats.
Individual sequences can be formatted to (e.g.) Genbank format as shown in the following examples.

For Sequence objects:
{{{
seq.to_seq.output(:genbank)
}}}

For Bio::!FlatFile entries:
{{{
entry.to_biosequence.output(:genbank)
}}}

Constants for available formats are:
  * Genbank :genbank


== 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 ===

The following example uses the MAFFT program to align four sequences
and then prints the result to the screen.
Please note that if the path to the MAFFT executable is properly set `mafft=Bio::MAFFT.new(options)` can be used instead of explicitly indicating the path as in the example. 

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

# 'seqs' is either an array of sequences or a multiple sequence 
# alignment. In general this is read in from a file as described in ?.
# For the purpose of this tutorial, it is generated in code.
seqs = ['MFQIPEFEPSEQEDSSSAER',
        'MGTPKQPSLAPAHALGLRKS',
        'PKQPSLAPAHALGLRKS',
        'MCSTSGCDLE'] 


# 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'

# 'seqs' is either an array of sequences or a multiple sequence 
# alignment. In general this is read in from a file as described in ?.
# For the purpose of this tutorial, it is generated in code.
seqs = ['MFQIPEFEPSEQEDSSSAER',
        'MGTPKQPSLAPAHALGLRKS',
        'PKQPSLAPAHALGLRKS',
        'MCSTSGCDLE']  

# 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 ===

_need more detail here..._

[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 ==

Oftentimes, multiple sequence to be used for phylogenetic inference are 'cleaned up' in some manner. For instance, some researchers prefer to delete columns with more than 50% gaps. The following code is an example of how to do that in !BioRuby.


_... to be done_

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

}}}


----

= Phylogenetic Trees =


== Phylogenetic Tree Input and Output ==


=== Reading in of Phylogenetic Trees ===



====Newick or New Hampshire Format====

_... to be done_

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

}}}

====phyloXML Format====

Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].

In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command: 

{{{
% gem install -r libxml-ruby
}}}

This example reads file "example.xml" and stores its [http://www.phyloxml.org/ phyloXML]-formatted trees in variable 'trees'.

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

# This creates new phyloXML parser.
trees = Bio::PhyloXML::Parser.new('example.xml')

# This prints the names of all trees in the file.
trees.each do |tree|
  puts tree.name
end

# If there are several trees in the file, you can access the one you wish via index.
tree = trees[3]

}}}



=== Writing of Phylogenetic Trees ===

====Newick or New Hampshire Format====

_... to be done_

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

}}}

====phyloXML Format====

Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].

In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command: 

{{{
% gem install -r libxml-ruby
}}}

This example writes trees 'tree1' and 'tree2' to file "tree.xml" in [http://www.phyloxml.org/ phyloXML] format.

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

# this creates new phyloXML writer.
writer = Bio::PhyloXML::Writer.new('tree.xml')

# Writes tree to the file "tree.xml".
writer.write(tree1)

# Adds another tree to the file.
writer.write(tree2)


}}}



== 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? ==


----

= Putting It All Together =

Example of a small "pipeline"-type program running a mininal phyogenetic analysis: starting with a set of sequences and ending with a phylogenetic tree.