1 #summary Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!
9 Tutorial for multiple sequence alignments and phylogenetic methods in [http://bioruby.open-bio.org/ BioRuby].
11 Eventually, this is expected to be placed on the official !BioRuby page.
13 Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute
16 Copyright (C) 2011 Christian M Zmasek
19 = Multiple Sequence Alignments =
22 == Multiple Sequence Alignment Input and Output ==
24 === Reading in a Multiple Sequence Alignment from a File ===
26 Reading in a clustalw formatted multiple sequence alignment:
32 # Reads in a clustalw formatted multiple sequence alignment
33 # from a file named "infile_clustalw.aln" and stores it in 'report'.
34 report = Bio::ClustalW::Report.new(File.read('infile_clustalw.aln'))
36 # Accesses the actual alignment.
37 align = report.alignment
39 # Goes through all sequences in 'align' and prints the
40 # actual molecular sequence.
48 === Writing a Multiple Sequence Alignment to a File ===
50 Writing a multiple sequence alignment in fasta format:
56 # Creates a new file named "outfile.fasta" and writes
57 # multiple sequence alignment 'align' to it in fasta format.
58 File.open('outfile.fasta', 'w') do |f|
59 f.write(align.output(:fasta))
64 Writing a multiple sequence alignment in clustalw format:
70 # Creates a new file named "outfile.aln" and writes
71 # multiple sequence alignment 'align' to it in clustal format.
72 File.open('outfile.aln', 'w') do |f|
73 f.write(align.output(:clustal))
78 == Calculating Multiple Sequence Alignments ==
80 !BioRuby can be used to execute a variety of multiple sequence alignment
81 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]).
82 In the following, examples for using the MAFFT and Muscle are shown.
87 The following example uses the MAFFT program to align four sequences
88 and then prints the result to the screen.
89 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.
95 # 'seqs' is either an array of sequences or a multiple sequence
96 # alignment. In general this is read in from a file as described in ?.
97 # For the purpose of this tutorial, it is generated in code.
98 seqs = ["KMLFGVVFFFGG",
104 # Calculates the alignment using the MAFFT program on the local
105 # machine with options '--maxiterate 1000 --localpair'
106 # and stores the result in 'report'.
107 options = ['--maxiterate', '1000', '--localpair']
108 mafft = Bio::MAFFT.new('path/to/mafft', options)
109 report = mafft.query_align(seqs)
111 # Accesses the actual alignment.
112 align = report.alignment
114 # Prints each sequence to the console.
115 align.each { |s| puts s.to_s }
121 * Katoh, Toh (2008) "Recent developments in the MAFFT multiple sequence alignment program" Briefings in Bioinformatics 9:286-298
123 * Katoh, Toh 2010 (2010) "Parallelization of the MAFFT multiple sequence alignment program" Bioinformatics 26:1899-1900
133 # 'seqs' is either an array of sequences or a multiple sequence
134 # alignment. In general this is read in from a file as described in ?.
135 # For the purpose of this tutorial, it is generated in code.
136 seqs = ["KMLFGVVFFFGG",
141 # Calculates the alignment using the Muscle program on the local
142 # machine with options '-quiet -maxiters 64'
143 # and stores the result in 'report'.
144 options = ['-quiet', '-maxiters', '64']
145 muscle = Bio::Muscle.new('path/to/muscle', options)
146 report = muscle.query_align(seqs)
148 # Accesses the actual alignment.
149 align = report.alignment
151 # Prints each sequence to the console.
152 align.each { |s| puts s.to_s }
158 * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797
160 === Other Programs ===
162 [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.
165 == Manipulating Multiple Sequence Alignments ==
167 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.
181 = Phylogenetic Trees =
183 == Phylogenetic Tree Input and Output ==
185 === Reading in of Phylogenetic Trees ===
195 Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
199 === Writing of Phylogenetic Trees ===
209 Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
213 == Phylogenetic Inference ==
215 _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..._
217 _What about pairwise distance calculation?_
221 == Maximum Likelihood ==
244 == Pairwise Distance Based Methods ==
262 == Support Calculation? ==
264 === Bootstrap Resampling? ===
269 = Analyzing Phylogenetic Trees =
274 == Gene Duplication Inference ==
276 _need to further test and then import GSoC 'SDI' work..._