#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!
+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 Alignments from a File ===
+=== Reading in a Multiple Sequence Alignment from a File ===
-_... to be done_
+The follow 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.
+align = report.alignment
+
+# Goes through all sequences in 'align' and prints the
+# actual molecular sequence.
+align.each do |entry|
+ puts entry.seq
+end
}}}
+
=== Writing a Multiple Sequence Alignment to a File ===
-_... to be done_
+
+The follow example shows how to writing a multiple sequence alignment in *FASTA*-format:
{{{
#!/usr/bin/env ruby
require 'bio'
+# Creates a new file named "outfile.fasta" and writes
+# multiple sequence alignment 'align' to it in fasta format.
+File.open('outfile.fasta', 'w') do |f|
+ f.write(align.output(:fasta))
+end
+}}}
+
+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 iPHYLIP's non-interleaved format:
+
+{{{
+f.write(align.output(:phylipnon))
}}}
-== Calculating Multiple Sequence Alignments ==
+== 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]).
+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 = ["KMLFGVVFFFGG",
+ "LMGGHHF",
+ "GKKKKGHHHGHRRRGR",
+ "KKKKGHHHGHRRRGR"]
+
+
# 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)
+report = mafft.query_align(seqs)
-# Accesses the actual alignment
+# Accesses the actual alignment.
align = report.alignment
# Prints each sequence to the console.
-report.align.each { |s| puts s.to_s }
-#
+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 = ["KMLFGVVFFFGG",
+ "LMGGHHF",
+ "GKKKKGHHHGHRRRGR",
+ "KKKKGHHHGHRRRGR"]
+
# 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)
+report = muscle.query_align(seqs)
-# Accesses the actual alignment
+# Accesses the actual alignment.
align = report.alignment
# Prints each sequence to the console.
-report.align.each { |s| puts s.to_s }
-#
+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:
+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_
}}}
+----
+
= Phylogenetic Trees =
== Phylogenetic Tree Input and Output ==
Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
+
+
=== Writing of Phylogenetic Trees ===
_... to be done_
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.*
+_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 ==
}}}
+=== PhyML ===
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
== Pairwise Distance Based Methods ==
=== FastME ===
}}}
+
+=== PHYLIP? ===
+
+
+
+== Support Calculation? ==
+
+=== Bootstrap Resampling? ===
+
+
+----
+
= Analyzing Phylogenetic Trees =
+== PAML ==
+
+
== Gene Duplication Inference ==
_need to further test and then import GSoC 'SDI' work..._
-== Others? ==
\ No newline at end of file
+== 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.
+
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff