1 #summary Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!
5 Tutorial for multiple sequence alignments and phylogenetic methods in !BioRuby -- under development!
8 = Multiple Sequence Alignments =
10 == Multiple Sequence Alignment Input and Output ==
12 === Reading in a Multiple Sequence Alignment from a File ===
23 === Writing a Multiple Sequence Alignment to a File ===
35 == Calculating Multiple Sequence Alignments ==
37 !BioRuby can be used to execute a variety of multiple sequence alignment
38 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]).
39 In the following, examples for using the MAFFT and Muscle are shown.
48 # Calculates the alignment using the MAFFT program on the local
49 # machine with options '--maxiterate 1000 --localpair'
50 # and stores the result in 'report'.
51 options = ['--maxiterate', '1000', '--localpair']
52 mafft = Bio::MAFFT.new('path/to/mafft', options)
53 report = mafft.query_align( seqs)
55 # Accesses the actual alignment
56 align = report.alignment
58 # Prints each sequence to the console.
59 report.align.each { |s| puts s.to_s }
65 * Katoh, Toh (2008) "Recent developments in the MAFFT multiple sequence alignment program" Briefings in Bioinformatics 9:286-298
67 * Katoh, Toh 2010 (2010) "Parallelization of the MAFFT multiple sequence alignment program" Bioinformatics 26:1899-1900
77 # Calculates the alignment using the Muscle program on the local
78 # machine with options '-quiet -maxiters 64'
79 # and stores the result in 'report'.
80 options = ['-quiet', '-maxiters', '64']
81 muscle = Bio::Muscle.new('path/to/muscle', options)
82 report = muscle.query_align( seqs)
84 # Accesses the actual alignment
85 align = report.alignment
87 # Prints each sequence to the console.
88 report.align.each { |s| puts s.to_s }
94 * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797
96 == Manipulating Multiple Sequence Alignments ==
98 It is probably a good idea to 'clean up' multiple sequence to be used
99 for phylogenetic inference. For instance, columns with more than 50% gaps can be deleted, like so:
111 = Phylogenetic Trees =
113 == Phylogenetic Tree Input and Output ==
115 === Reading in of Phylogenetic Trees ===
125 Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
127 === Writing of Phylogenetic Trees ===
137 Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
140 == Phylogenetic Inference ==
142 _Currently !BioRuby does not contain wrappers for phylogenetic inference programs, thus I am progress of writing a RAxML wrapper followed by a wrapper for FastMA..._
144 == Maximum Likelihood ==
157 == Pairwise Distance Based Methods ==
170 = Analyzing Phylogenetic Trees =
172 == Gene Duplication Inference ==
174 _need to further test and then import GSoC 'SDI' work..._