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.
46 The following example shows how to read in a *FASTA*-formatted multiple sequence file.
51 # Reads in a FASTA-formatted multiple sequence alignment (which does
52 # not have to be aligned, though) and stores its sequences in
55 fasta_seqs = Bio::Alignment::MultiFastaFormat.new(File.open('infile.fasta').read)
56 fasta_seqs.entries.each do |seq|
60 # Creates a multiple sequence alignment (possibly unaligned) named
61 # 'seqs' from array 'seq_ary'.
62 seqs = Bio::Alignment.new(seq_ary)
64 # Prints each sequence to the console.
65 seqs.each { |seq| puts seq.to_s }
67 # Writes multiple sequence alignment (possibly unaligned) 'seqs'
68 # to a file in PHYLIP format.
69 File.open('out1.phylip', 'w') do |f|
70 f.write(seqs.output(:phylip))
74 Relevant API documentation:
76 * [http://bioruby.open-bio.org/rdoc/classes/Bio/ClustalW/Report.html Bio::ClustalW::Report]
77 * [http://bioruby.open-bio.org/rdoc/classes/Bio/Alignment.html Bio::Alignment]
78 * [http://bioruby.open-bio.org/rdoc/classes/Bio/Sequence.html Bio::Sequence]
80 === Writing a Multiple Sequence Alignment to a File ===
83 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').
89 # Creates a new file named "outfile.fasta" and writes
90 # multiple sequence alignment 'msa' to it in fasta format.
91 File.open('outfile.fasta', 'w') do |f|
92 f.write(msa.output(:fasta))
96 ==== Setting the Output Format ====
98 The following symbols determine the output format:
100 * `:clustal` for ClustalW
102 * `:phylip` for PHYLIP interleaved (will truncate sequence names to no more than 10 characters)
103 * `:phylipnon` for PHYLIP non-interleaved (will truncate sequence names to no more than 10 characters)
105 * `:molphy` for Molphy
108 For example, the following writes in PHYLIP's non-interleaved format:
111 f.write(align.output(:phylipnon))
115 === Formatting of Individual Sequences ===
117 !BioRuby can format molecular sequences in a variety of formats.
118 Individual sequences can be formatted to (e.g.) Genbank format as shown in the following examples.
120 For Sequence objects:
122 seq.to_seq.output(:genbank)
125 For Bio::!FlatFile entries:
127 entry.to_biosequence.output(:genbank)
130 The following symbols determine the output format:
131 * `:genbank` for Genbank
134 * `:fasta_ncbi` for NCBI-type FASTA
135 * `:raw` for raw sequence
136 * `:fastq` for FASTQ (includes quality scores)
137 * `:fastq_sanger` for Sanger-type FASTQ
138 * `:fastq_solexa` for Solexa-type FASTQ
139 * `:fastq_illumina` for Illumina-type FASTQ
141 == Calculating Multiple Sequence Alignments ==
143 !BioRuby can be used to execute a variety of multiple sequence alignment
144 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]).
145 In the following, examples for using the MAFFT and Muscle are shown.
150 The following example uses the MAFFT program to align four sequences
151 and then prints the result to the screen.
152 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.
158 # 'seqs' is either an array of sequences or a multiple sequence
159 # alignment. In general this is read in from a file as described in ?.
160 # For the purpose of this tutorial, it is generated in code.
161 seqs = ['MFQIPEFEPSEQEDSSSAER',
162 'MGTPKQPSLAPAHALGLRKS',
167 # Calculates the alignment using the MAFFT program on the local
168 # machine with options '--maxiterate 1000 --localpair'
169 # and stores the result in 'report'.
170 options = ['--maxiterate', '1000', '--localpair']
171 mafft = Bio::MAFFT.new('path/to/mafft', options)
172 report = mafft.query_align(seqs)
174 # Accesses the actual alignment.
175 align = report.alignment
177 # Prints each sequence to the console.
178 align.each { |s| puts s.to_s }
184 * Katoh, Toh (2008) "Recent developments in the MAFFT multiple sequence alignment program" Briefings in Bioinformatics 9:286-298
186 * Katoh, Toh 2010 (2010) "Parallelization of the MAFFT multiple sequence alignment program" Bioinformatics 26:1899-1900
196 # 'seqs' is either an array of sequences or a multiple sequence
197 # alignment. In general this is read in from a file as described in ?.
198 # For the purpose of this tutorial, it is generated in code.
199 seqs = ['MFQIPEFEPSEQEDSSSAER',
200 'MGTPKQPSLAPAHALGLRKS',
204 # Calculates the alignment using the Muscle program on the local
205 # machine with options '-quiet -maxiters 64'
206 # and stores the result in 'report'.
207 options = ['-quiet', '-maxiters', '64']
208 muscle = Bio::Muscle.new('path/to/muscle', options)
209 report = muscle.query_align(seqs)
211 # Accesses the actual alignment.
212 align = report.alignment
214 # Prints each sequence to the console.
215 align.each { |s| puts s.to_s }
221 * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797
223 === Other Programs ===
225 _need more detail here..._
227 [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.
231 == Manipulating Multiple Sequence Alignments ==
233 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.
247 = Phylogenetic Trees =
250 == Phylogenetic Tree Input and Output ==
253 === Reading in of Phylogenetic Trees ===
257 ====Newick or New Hampshire Format====
267 ====phyloXML Format====
269 Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
271 In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command:
274 % gem install -r libxml-ruby
277 This example reads file "example.xml" and stores its [http://www.phyloxml.org/ phyloXML]-formatted trees in variable 'trees'.
283 # This creates new phyloXML parser.
284 trees = Bio::PhyloXML::Parser.new('example.xml')
286 # This prints the names of all trees in the file.
291 # If there are several trees in the file, you can access the one you wish via index.
307 === Writing of Phylogenetic Trees ===
309 ====Newick or New Hampshire Format====
319 ====phyloXML Format====
321 Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
323 In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command:
326 % gem install -r libxml-ruby
329 This example writes trees 'tree1' and 'tree2' to file "tree.xml" in [http://www.phyloxml.org/ phyloXML] format.
335 # this creates new phyloXML writer.
336 writer = Bio::PhyloXML::Writer.new('tree.xml')
338 # Writes tree to the file "tree.xml".
341 # Adds another tree to the file.
359 = Phylogenetic Inference =
361 _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..._
363 == Optimality Criteria Based on Character Data ==
365 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.
367 === Maximum Likelihood ===
390 === Maximum Parsimony ===
392 Currently no direct support in !BioRuby.
395 === Bayesian Inference ===
397 Currently no direct support in !BioRuby.
400 == Pairwise Distance Based Methods ==
402 === Pairwise Sequence Distance Estimation ===
413 === Optimality Criteria Based on Pairwise Distances ===
416 ==== Minimal Evolution: FastME ====
426 === Algorithmic Methods Based on Pairwise Distances ===
428 ==== Neighbor Joining and Related Methods ====
444 == Support Calculation? ==
446 === Bootstrap Resampling? ===
451 = Analyzing Phylogenetic Trees =
456 == Gene Duplication Inference ==
458 _need to further test and then import GSoC 'SDI' work..._
466 = Putting It All Together =
468 Example of a small "pipeline"-type program running a mininal phyogenetic analysis: starting with a set of sequences and ending with a phylogenetic tree.