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 This automatically determines the format
28 ff = Bio::FlatFile.auto('bcl2.fasta')
29 ff.each_entry do |entry|
30 puts entry.entry_id # identifier of the entry
31 puts entry.definition # definition of the entry
32 puts entry.seq # sequence data of the entry
36 ==== ClustalW Format ====
38 The following example shows how to read in a *ClustalW*-formatted multiple sequence alignment.
44 # Reads in a ClustalW-formatted multiple sequence alignment
45 # from a file named "infile_clustalw.aln" and stores it in 'report'.
46 report = Bio::ClustalW::Report.new(File.read('infile_clustalw.aln'))
48 # Accesses the actual alignment.
49 msa = report.alignment
51 # Goes through all sequences in 'msa' and prints the
52 # actual molecular sequence.
58 ==== FASTA Format ====
60 The following example shows how to read in a *FASTA*-formatted multiple sequence file. (_This seems a little clumsy, I wonder if there is a more direct way, avoiding the creation of an array.)
65 # Reads in a FASTA-formatted multiple sequence alignment (which does
66 # not have to be aligned, though) and stores its sequences in
69 fasta_seqs = Bio::Alignment::MultiFastaFormat.new(File.open('infile.fasta').read)
70 fasta_seqs.entries.each do |seq|
74 # Creates a multiple sequence alignment (possibly unaligned) named
75 # 'seqs' from array 'seq_ary'.
76 seqs = Bio::Alignment.new(seq_ary)
78 # Prints each sequence to the console.
79 seqs.each { |seq| puts seq.to_s }
81 # Writes multiple sequence alignment (possibly unaligned) 'seqs'
82 # to a file in PHYLIP format.
83 File.open('outfile.phylip', 'w') do |f|
84 f.write(seqs.output(:phylip))
88 Relevant API documentation:
90 * [http://bioruby.open-bio.org/rdoc/classes/Bio/ClustalW/Report.html Bio::ClustalW::Report]
91 * [http://bioruby.open-bio.org/rdoc/classes/Bio/Alignment.html Bio::Alignment]
92 * [http://bioruby.open-bio.org/rdoc/classes/Bio/Sequence.html Bio::Sequence]
94 === Writing a Multiple Sequence Alignment to a File ===
97 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').
103 # Creates a new file named "outfile.fasta" and writes
104 # multiple sequence alignment 'msa' to it in fasta format.
105 File.open('outfile.fasta', 'w') do |f|
106 f.write(msa.output(:fasta))
110 ==== Setting the Output Format ====
112 The following symbols determine the output format:
114 * `:clustal` for ClustalW
116 * `:phylip` for PHYLIP interleaved (will truncate sequence names to no more than 10 characters)
117 * `:phylipnon` for PHYLIP non-interleaved (will truncate sequence names to no more than 10 characters)
119 * `:molphy` for Molphy
122 For example, the following writes in PHYLIP's non-interleaved format:
125 f.write(align.output(:phylipnon))
129 === Formatting of Individual Sequences ===
131 !BioRuby can format molecular sequences in a variety of formats.
132 Individual sequences can be formatted to (e.g.) Genbank format as shown in the following examples.
134 For Sequence objects:
136 seq.to_seq.output(:genbank)
139 For Bio::!FlatFile entries:
141 entry.to_biosequence.output(:genbank)
144 The following symbols determine the output format:
145 * `:genbank` for Genbank
148 * `:fasta_ncbi` for NCBI-type FASTA
149 * `:raw` for raw sequence
150 * `:fastq` for FASTQ (includes quality scores)
151 * `:fastq_sanger` for Sanger-type FASTQ
152 * `:fastq_solexa` for Solexa-type FASTQ
153 * `:fastq_illumina` for Illumina-type FASTQ
155 == Calculating Multiple Sequence Alignments ==
157 !BioRuby can be used to execute a variety of multiple sequence alignment
158 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]).
159 In the following, examples for using the MAFFT and Muscle are shown.
164 The following example uses the MAFFT program to align four sequences
165 and then prints the result to the screen.
166 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.
172 # 'seqs' is either an array of sequences or a multiple sequence
173 # alignment. In general this is read in from a file as described in ?.
174 # For the purpose of this tutorial, it is generated in code.
175 seqs = ['MFQIPEFEPSEQEDSSSAER',
176 'MGTPKQPSLAPAHALGLRKS',
181 # Calculates the alignment using the MAFFT program on the local
182 # machine with options '--maxiterate 1000 --localpair'
183 # and stores the result in 'report'.
184 options = ['--maxiterate', '1000', '--localpair']
185 mafft = Bio::MAFFT.new('path/to/mafft', options)
186 report = mafft.query_align(seqs)
188 # Accesses the actual alignment.
189 align = report.alignment
191 # Prints each sequence to the console.
192 align.each { |s| puts s.to_s }
198 * Katoh, Toh (2008) "Recent developments in the MAFFT multiple sequence alignment program" Briefings in Bioinformatics 9:286-298
200 * Katoh, Toh 2010 (2010) "Parallelization of the MAFFT multiple sequence alignment program" Bioinformatics 26:1899-1900
210 # 'seqs' is either an array of sequences or a multiple sequence
211 # alignment. In general this is read in from a file as described in ?.
212 # For the purpose of this tutorial, it is generated in code.
213 seqs = ['MFQIPEFEPSEQEDSSSAER',
214 'MGTPKQPSLAPAHALGLRKS',
218 # Calculates the alignment using the Muscle program on the local
219 # machine with options '-quiet -maxiters 64'
220 # and stores the result in 'report'.
221 options = ['-quiet', '-maxiters', '64']
222 muscle = Bio::Muscle.new('path/to/muscle', options)
223 report = muscle.query_align(seqs)
225 # Accesses the actual alignment.
226 align = report.alignment
228 # Prints each sequence to the console.
229 align.each { |s| puts s.to_s }
235 * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797
237 === Other Programs ===
239 _need more detail here..._
241 [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.
245 == Manipulating Multiple Sequence Alignments ==
247 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.
261 = Phylogenetic Trees =
264 == Phylogenetic Tree Input and Output ==
267 === Reading in of Phylogenetic Trees ===
271 ====Newick or New Hampshire Format====
281 ====phyloXML Format====
283 Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
285 In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command:
288 % gem install -r libxml-ruby
291 This example reads file "example.xml" and stores its [http://www.phyloxml.org/ phyloXML]-formatted trees in variable 'trees'.
297 # This creates new phyloXML parser.
298 trees = Bio::PhyloXML::Parser.new('example.xml')
300 # This prints the names of all trees in the file.
305 # If there are several trees in the file, you can access the one you wish via index.
321 === Writing of Phylogenetic Trees ===
323 ====Newick or New Hampshire Format====
333 ====phyloXML Format====
335 Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
337 In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command:
340 % gem install -r libxml-ruby
343 This example writes trees 'tree1' and 'tree2' to file "tree.xml" in [http://www.phyloxml.org/ phyloXML] format.
349 # this creates new phyloXML writer.
350 writer = Bio::PhyloXML::Writer.new('tree.xml')
352 # Writes tree to the file "tree.xml".
355 # Adds another tree to the file.
373 = Phylogenetic Inference =
375 _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..._
377 == Optimality Criteria Based on Character Data ==
379 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.
381 === Maximum Likelihood ===
404 === Maximum Parsimony ===
406 Currently no direct support in !BioRuby.
409 === Bayesian Inference ===
411 Currently no direct support in !BioRuby.
414 == Pairwise Distance Based Methods ==
416 === Pairwise Sequence Distance Estimation ===
427 === Optimality Criteria Based on Pairwise Distances ===
430 ==== Minimal Evolution: FastME ====
440 === Algorithmic Methods Based on Pairwise Distances ===
442 ==== Neighbor Joining and Related Methods ====
458 == Support Calculation? ==
460 === Bootstrap Resampling? ===
465 = Analyzing Phylogenetic Trees =
470 == Gene Duplication Inference ==
472 _need to further test and then import GSoC 'SDI' work..._
480 = Putting It All Together =
482 Example of a small "pipeline"-type program running a mininal phyogenetic analysis: starting with a set of sequences and ending with a phylogenetic tree.