1 #summary Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!
7 Tutorial for multiple sequence alignments and phylogenetic methods in !BioRuby -- under development!
11 = Multiple Sequence Alignments =
14 == Multiple Sequence Alignment Input and Output ==
16 === Reading in a Multiple Sequence Alignment from a File ===
28 === Writing a Multiple Sequence Alignment to a File ===
40 == Calculating Multiple Sequence Alignments ==
42 !BioRuby can be used to execute a variety of multiple sequence alignment
43 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]).
44 In the following, examples for using the MAFFT and Muscle are shown.
53 # Calculates the alignment using the MAFFT program on the local
54 # machine with options '--maxiterate 1000 --localpair'
55 # and stores the result in 'report'.
56 options = ['--maxiterate', '1000', '--localpair']
57 mafft = Bio::MAFFT.new('path/to/mafft', options)
58 report = mafft.query_align(seqs)
60 # Accesses the actual alignment
61 align = report.alignment
63 # Prints each sequence to the console.
64 align.each { |s| puts s.to_s }
70 * Katoh, Toh (2008) "Recent developments in the MAFFT multiple sequence alignment program" Briefings in Bioinformatics 9:286-298
72 * Katoh, Toh 2010 (2010) "Parallelization of the MAFFT multiple sequence alignment program" Bioinformatics 26:1899-1900
82 # Calculates the alignment using the Muscle program on the local
83 # machine with options '-quiet -maxiters 64'
84 # and stores the result in 'report'.
85 options = ['-quiet', '-maxiters', '64']
86 muscle = Bio::Muscle.new('path/to/muscle', options)
87 report = muscle.query_align(seqs)
89 # Accesses the actual alignment
90 align = report.alignment
92 # Prints each sequence to the console.
93 align.each { |s| puts s.to_s }
99 * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797
103 == Manipulating Multiple Sequence Alignments ==
105 It is probably a good idea to 'clean up' multiple sequence to be used
106 for phylogenetic inference. For instance, columns with more than 50% gaps can be deleted, like so:
119 = Phylogenetic Trees =
121 == Phylogenetic Tree Input and Output ==
123 === Reading in of Phylogenetic Trees ===
133 Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
137 === Writing of Phylogenetic Trees ===
147 Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
151 == Phylogenetic Inference ==
153 _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..._
155 _What about pairwise distance calculation?_
159 == Maximum Likelihood ==
173 == Pairwise Distance Based Methods ==
191 == Support Calculation? ==
193 === Bootstrap Resampling? ===
197 = Analyzing Phylogenetic Trees =
202 == Gene Duplication Inference ==
204 _need to further test and then import GSoC 'SDI' work..._