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 Relevant API documentation:
48 * [http://bioruby.open-bio.org/rdoc/classes/Bio/ClustalW/Report.html Bio::ClustalW::Report]
49 * [http://bioruby.open-bio.org/rdoc/classes/Bio/Alignment.html Bio::Alignment]
50 * [http://bioruby.open-bio.org/rdoc/classes/Bio/Sequence.html Bio::Sequence]
52 === Writing a Multiple Sequence Alignment to a File ===
55 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').
61 # Creates a new file named "outfile.fasta" and writes
62 # multiple sequence alignment 'msa' to it in fasta format.
63 File.open('outfile.fasta', 'w') do |f|
64 f.write(msa.output(:fasta))
68 ==== Setting the Output Format ====
70 The following symbols determine the output format:
72 * `:clustal` for ClustalW
74 * `:phylip` for PHYLIP interleaved (will truncate sequence names to no more than 10 characters)
75 * `:phylipnon` for PHYLIP non-interleaved (will truncate sequence names to no more than 10 characters)
77 * `:molphy` for Molphy
80 For example, the following writes in PHYLIP's non-interleaved format:
83 f.write(align.output(:phylipnon))
87 === Formatting of Individual Sequences ===
89 !BioRuby can format molecular sequences in a variety of formats.
90 Individual sequences can be formatted to (e.g.) Genbank format as shown in the following examples.
94 seq.to_seq.output(:genbank)
97 For Bio::!FlatFile entries:
99 entry.to_biosequence.output(:genbank)
102 The following symbols determine the output format:
103 * `:genbank` for Genbank
106 * `:fasta_ncbi` for NCBI-type FASTA
107 * `:raw` for raw sequence
108 * `:fastq` for FASTQ (includes quality scores)
109 * `:fastq_sanger` for Sanger-type FASTQ
110 * `:fastq_solexa` for Solexa-type FASTQ
111 * `:fastq_illumina` for Illumina-type FASTQ
113 == Calculating Multiple Sequence Alignments ==
115 !BioRuby can be used to execute a variety of multiple sequence alignment
116 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]).
117 In the following, examples for using the MAFFT and Muscle are shown.
122 The following example uses the MAFFT program to align four sequences
123 and then prints the result to the screen.
124 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.
130 # 'seqs' is either an array of sequences or a multiple sequence
131 # alignment. In general this is read in from a file as described in ?.
132 # For the purpose of this tutorial, it is generated in code.
133 seqs = ['MFQIPEFEPSEQEDSSSAER',
134 'MGTPKQPSLAPAHALGLRKS',
139 # Calculates the alignment using the MAFFT program on the local
140 # machine with options '--maxiterate 1000 --localpair'
141 # and stores the result in 'report'.
142 options = ['--maxiterate', '1000', '--localpair']
143 mafft = Bio::MAFFT.new('path/to/mafft', options)
144 report = mafft.query_align(seqs)
146 # Accesses the actual alignment.
147 align = report.alignment
149 # Prints each sequence to the console.
150 align.each { |s| puts s.to_s }
156 * Katoh, Toh (2008) "Recent developments in the MAFFT multiple sequence alignment program" Briefings in Bioinformatics 9:286-298
158 * Katoh, Toh 2010 (2010) "Parallelization of the MAFFT multiple sequence alignment program" Bioinformatics 26:1899-1900
168 # 'seqs' is either an array of sequences or a multiple sequence
169 # alignment. In general this is read in from a file as described in ?.
170 # For the purpose of this tutorial, it is generated in code.
171 seqs = ['MFQIPEFEPSEQEDSSSAER',
172 'MGTPKQPSLAPAHALGLRKS',
176 # Calculates the alignment using the Muscle program on the local
177 # machine with options '-quiet -maxiters 64'
178 # and stores the result in 'report'.
179 options = ['-quiet', '-maxiters', '64']
180 muscle = Bio::Muscle.new('path/to/muscle', options)
181 report = muscle.query_align(seqs)
183 # Accesses the actual alignment.
184 align = report.alignment
186 # Prints each sequence to the console.
187 align.each { |s| puts s.to_s }
193 * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797
195 === Other Programs ===
197 _need more detail here..._
199 [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.
203 == Manipulating Multiple Sequence Alignments ==
205 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.
219 = Phylogenetic Trees =
222 == Phylogenetic Tree Input and Output ==
225 === Reading in of Phylogenetic Trees ===
229 ====Newick or New Hampshire Format====
239 ====phyloXML Format====
241 Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
243 In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command:
246 % gem install -r libxml-ruby
249 This example reads file "example.xml" and stores its [http://www.phyloxml.org/ phyloXML]-formatted trees in variable 'trees'.
255 # This creates new phyloXML parser.
256 trees = Bio::PhyloXML::Parser.new('example.xml')
258 # This prints the names of all trees in the file.
263 # If there are several trees in the file, you can access the one you wish via index.
279 === Writing of Phylogenetic Trees ===
281 ====Newick or New Hampshire Format====
291 ====phyloXML Format====
293 Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
295 In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command:
298 % gem install -r libxml-ruby
301 This example writes trees 'tree1' and 'tree2' to file "tree.xml" in [http://www.phyloxml.org/ phyloXML] format.
307 # this creates new phyloXML writer.
308 writer = Bio::PhyloXML::Writer.new('tree.xml')
310 # Writes tree to the file "tree.xml".
313 # Adds another tree to the file.
331 = Phylogenetic Inference =
333 _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..._
335 == Optimality Criteria Based on Character Data ==
337 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.
339 === Maximum Likelihood ===
362 === Maximum Parsimony ===
364 Currently no direct support in !BioRuby.
367 === Bayesian Inference ===
369 Currently no direct support in !BioRuby.
372 == Pairwise Distance Based Methods ==
374 === Pairwise Sequence Distance Estimation ===
385 === Optimality Criteria Based on Pairwise Distances ===
388 ==== Minimal Evolution: FastME ====
398 === Algorithmic Methods Based on Pairwise Distances ===
400 ==== Neighbor Joining and Related Methods ====
416 == Support Calculation? ==
418 === Bootstrap Resampling? ===
423 = Analyzing Phylogenetic Trees =
428 == Gene Duplication Inference ==
430 _need to further test and then import GSoC 'SDI' work..._
438 = Putting It All Together =
440 Example of a small "pipeline"-type program running a mininal phyogenetic analysis: starting with a set of sequences and ending with a phylogenetic tree.