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. All rights reserved.
19 = Multiple Sequence Alignment =
22 == Multiple Sequence Alignment Input and Output ==
24 === Reading in a Multiple Sequence Alignment from a File ===
26 The following 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 msa = report.alignment
39 # Goes through all sequences in 'msa' and prints the
40 # actual molecular sequence.
48 # Reads in a Fasta-formatted multiple sequence alignment (which does
49 # not have to be aligned, though) and stores its sequences in
52 fasta_seqs = Bio::Alignment::MultiFastaFormat.new(File.open('bcl2.fasta').read)
53 fasta_seqs.entries.each do |seq|
57 # Creates a multiple sequence alignment (possibly unaligned) named
58 # 'seqs' from array 'seq_ary'.
59 seqs = Bio::Alignment.new( seq_ary )
60 seqs.each { |seq| puts seq.to_s }
65 # Writes multiple sequence alignment (possibly unaligned) 'seqs'
66 # to a file in phylip format.
67 File.open('out1.phylip', 'w') do |f|
68 f.write(seqs.output(:phylip))
72 Relevant API documentation:
74 * [http://bioruby.open-bio.org/rdoc/classes/Bio/ClustalW/Report.html Bio::ClustalW::Report]
75 * [http://bioruby.open-bio.org/rdoc/classes/Bio/Alignment.html Bio::Alignment]
76 * [http://bioruby.open-bio.org/rdoc/classes/Bio/Sequence.html Bio::Sequence]
78 === Writing a Multiple Sequence Alignment to a File ===
81 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').
87 # Creates a new file named "outfile.fasta" and writes
88 # multiple sequence alignment 'msa' to it in fasta format.
89 File.open('outfile.fasta', 'w') do |f|
90 f.write(msa.output(:fasta))
94 ==== Setting the Output Format ====
96 The following symbols determine the output format:
98 * `:clustal` for ClustalW
100 * `:phylip` for PHYLIP interleaved (will truncate sequence names to no more than 10 characters)
101 * `:phylipnon` for PHYLIP non-interleaved (will truncate sequence names to no more than 10 characters)
103 * `:molphy` for Molphy
106 For example, the following writes in PHYLIP's non-interleaved format:
109 f.write(align.output(:phylipnon))
113 === Formatting of Individual Sequences ===
115 !BioRuby can format molecular sequences in a variety of formats.
116 Individual sequences can be formatted to (e.g.) Genbank format as shown in the following examples.
118 For Sequence objects:
120 seq.to_seq.output(:genbank)
123 For Bio::!FlatFile entries:
125 entry.to_biosequence.output(:genbank)
128 The following symbols determine the output format:
129 * `:genbank` for Genbank
132 * `:fasta_ncbi` for NCBI-type FASTA
133 * `:raw` for raw sequence
134 * `:fastq` for FASTQ (includes quality scores)
135 * `:fastq_sanger` for Sanger-type FASTQ
136 * `:fastq_solexa` for Solexa-type FASTQ
137 * `:fastq_illumina` for Illumina-type FASTQ
139 == Calculating Multiple Sequence Alignments ==
141 !BioRuby can be used to execute a variety of multiple sequence alignment
142 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]).
143 In the following, examples for using the MAFFT and Muscle are shown.
148 The following example uses the MAFFT program to align four sequences
149 and then prints the result to the screen.
150 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.
156 # 'seqs' is either an array of sequences or a multiple sequence
157 # alignment. In general this is read in from a file as described in ?.
158 # For the purpose of this tutorial, it is generated in code.
159 seqs = ['MFQIPEFEPSEQEDSSSAER',
160 'MGTPKQPSLAPAHALGLRKS',
165 # Calculates the alignment using the MAFFT program on the local
166 # machine with options '--maxiterate 1000 --localpair'
167 # and stores the result in 'report'.
168 options = ['--maxiterate', '1000', '--localpair']
169 mafft = Bio::MAFFT.new('path/to/mafft', options)
170 report = mafft.query_align(seqs)
172 # Accesses the actual alignment.
173 align = report.alignment
175 # Prints each sequence to the console.
176 align.each { |s| puts s.to_s }
182 * Katoh, Toh (2008) "Recent developments in the MAFFT multiple sequence alignment program" Briefings in Bioinformatics 9:286-298
184 * Katoh, Toh 2010 (2010) "Parallelization of the MAFFT multiple sequence alignment program" Bioinformatics 26:1899-1900
194 # 'seqs' is either an array of sequences or a multiple sequence
195 # alignment. In general this is read in from a file as described in ?.
196 # For the purpose of this tutorial, it is generated in code.
197 seqs = ['MFQIPEFEPSEQEDSSSAER',
198 'MGTPKQPSLAPAHALGLRKS',
202 # Calculates the alignment using the Muscle program on the local
203 # machine with options '-quiet -maxiters 64'
204 # and stores the result in 'report'.
205 options = ['-quiet', '-maxiters', '64']
206 muscle = Bio::Muscle.new('path/to/muscle', options)
207 report = muscle.query_align(seqs)
209 # Accesses the actual alignment.
210 align = report.alignment
212 # Prints each sequence to the console.
213 align.each { |s| puts s.to_s }
219 * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797
221 === Other Programs ===
223 _need more detail here..._
225 [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.
229 == Manipulating Multiple Sequence Alignments ==
231 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.
245 = Phylogenetic Trees =
248 == Phylogenetic Tree Input and Output ==
251 === Reading in of Phylogenetic Trees ===
255 ====Newick or New Hampshire Format====
265 ====phyloXML Format====
267 Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
269 In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command:
272 % gem install -r libxml-ruby
275 This example reads file "example.xml" and stores its [http://www.phyloxml.org/ phyloXML]-formatted trees in variable 'trees'.
281 # This creates new phyloXML parser.
282 trees = Bio::PhyloXML::Parser.new('example.xml')
284 # This prints the names of all trees in the file.
289 # If there are several trees in the file, you can access the one you wish via index.
305 === Writing of Phylogenetic Trees ===
307 ====Newick or New Hampshire Format====
317 ====phyloXML Format====
319 Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
321 In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command:
324 % gem install -r libxml-ruby
327 This example writes trees 'tree1' and 'tree2' to file "tree.xml" in [http://www.phyloxml.org/ phyloXML] format.
333 # this creates new phyloXML writer.
334 writer = Bio::PhyloXML::Writer.new('tree.xml')
336 # Writes tree to the file "tree.xml".
339 # Adds another tree to the file.
357 = Phylogenetic Inference =
359 _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..._
361 == Optimality Criteria Based on Character Data ==
363 Character data based methods work directly on molecular sequences and thus do not require the calculation of pairwise distances but tend to be time consuming and sensitive to errors in the multiple sequence alignment.
365 === Maximum Likelihood ===
388 === Maximum Parsimony ===
390 Currently no direct support in !BioRuby.
393 === Bayesian Inference ===
395 Currently no direct support in !BioRuby.
398 == Pairwise Distance Based Methods ==
400 === Pairwise Sequence Distance Estimation ===
411 === Optimality Criteria Based on Pairwise Distances ===
414 ==== Minimal Evolution: FastME ====
424 === Algorithmic Methods Based on Pairwise Distances ===
426 ==== Neighbor Joining and Related Methods ====
442 == Support Calculation? ==
444 === Bootstrap Resampling? ===
449 = Analyzing Phylogenetic Trees =
454 == Gene Duplication Inference ==
456 _need to further test and then import GSoC 'SDI' work..._
464 = Putting It All Together =
466 Example of a small "pipeline"-type program running a mininal phyogenetic analysis: starting with a set of sequences and ending with a phylogenetic tree.