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 The follow example shows how to read 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 ===
51 The follow example shows how to writing a multiple sequence alignment in *FASTA*-format:
57 # Creates a new file named "outfile.fasta" and writes
58 # multiple sequence alignment 'align' to it in fasta format.
59 File.open('outfile.fasta', 'w') do |f|
60 f.write(align.output(:fasta))
64 The following constants determine the output format
66 * ClustalW: `:clustal`
68 * PHYLIP interleaved (will truncate sequence names to no more than 10 characters): `:phylip`
69 * PHYLIP non-interleaved (will truncate sequence names to no more than 10 characters): `:phylipnon`
74 For example, the following writes iPHYLIP's non-interleaved format:
77 f.write(align.output(:phylipnon))
82 == Calculating Multiple Sequence Alignments ==
84 !BioRuby can be used to execute a variety of multiple sequence alignment
85 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]).
86 In the following, examples for using the MAFFT and Muscle are shown.
91 The following example uses the MAFFT program to align four sequences
92 and then prints the result to the screen.
93 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.
99 # 'seqs' is either an array of sequences or a multiple sequence
100 # alignment. In general this is read in from a file as described in ?.
101 # For the purpose of this tutorial, it is generated in code.
102 seqs = ["KMLFGVVFFFGG",
108 # Calculates the alignment using the MAFFT program on the local
109 # machine with options '--maxiterate 1000 --localpair'
110 # and stores the result in 'report'.
111 options = ['--maxiterate', '1000', '--localpair']
112 mafft = Bio::MAFFT.new('path/to/mafft', options)
113 report = mafft.query_align(seqs)
115 # Accesses the actual alignment.
116 align = report.alignment
118 # Prints each sequence to the console.
119 align.each { |s| puts s.to_s }
125 * Katoh, Toh (2008) "Recent developments in the MAFFT multiple sequence alignment program" Briefings in Bioinformatics 9:286-298
127 * Katoh, Toh 2010 (2010) "Parallelization of the MAFFT multiple sequence alignment program" Bioinformatics 26:1899-1900
137 # 'seqs' is either an array of sequences or a multiple sequence
138 # alignment. In general this is read in from a file as described in ?.
139 # For the purpose of this tutorial, it is generated in code.
140 seqs = ["KMLFGVVFFFGG",
145 # Calculates the alignment using the Muscle program on the local
146 # machine with options '-quiet -maxiters 64'
147 # and stores the result in 'report'.
148 options = ['-quiet', '-maxiters', '64']
149 muscle = Bio::Muscle.new('path/to/muscle', options)
150 report = muscle.query_align(seqs)
152 # Accesses the actual alignment.
153 align = report.alignment
155 # Prints each sequence to the console.
156 align.each { |s| puts s.to_s }
162 * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797
164 === Other Programs ===
166 [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.
169 == Manipulating Multiple Sequence Alignments ==
171 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.
185 = Phylogenetic Trees =
187 == Phylogenetic Tree Input and Output ==
189 === Reading in of Phylogenetic Trees ===
199 Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
203 === Writing of Phylogenetic Trees ===
213 Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
217 == Phylogenetic Inference ==
219 _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..._
221 _What about pairwise distance calculation?_
225 == Maximum Likelihood ==
248 == Pairwise Distance Based Methods ==
266 == Support Calculation? ==
268 === Bootstrap Resampling? ===
273 = Analyzing Phylogenetic Trees =
278 == Gene Duplication Inference ==
280 _need to further test and then import GSoC 'SDI' work..._
288 = Putting It All Together =
290 Example of a small "pipeline"-type program running a mininal phyogenetic analysis: starting with a set of sequences and ending with a phylogenetic tree.