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 == Reading in a Multiple Sequence Alignments from a File ==
21 == Writing a Multiple Sequence Alignment to a File ==
33 == Calculating Multiple Sequence Alignments ==
35 !BioRuby can be used to execute a variety of multiple sequence alignment
36 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]).
37 In the following, examples for using the MAFFT and Muscle are shown.
46 # Calculates the alignment using the MAFFT program on the local
47 # machine with options '--maxiterate 1000 --localpair'
48 # and stores the result in 'report'.
49 options = ['--maxiterate', '1000', '--localpair']
50 mafft = Bio::MAFFT.new('path/to/mafft', options)
51 report = mafft.query_align( seqs)
53 # Accesses the actual alignment
54 align = report.alignment
56 # Prints each sequence to the console.
57 report.align.each { |s| puts s.to_s }
68 # Calculates the alignment using the Muscle program on the local
69 # machine with options '-quiet -maxiters 64'
70 # and stores the result in 'report'.
71 options = ['-quiet', '-maxiters', '64']
72 muscle = Bio::Muscle.new('path/to/muscle', options)
73 report = muscle.query_align( seqs)
75 # Accesses the actual alignment
76 align = report.alignment
78 # Prints each sequence to the console.
79 report.align.each { |s| puts s.to_s }
84 == Manipulating Multiple Sequence Alignments ==
86 It is probably a good idea to 'clean up' multiple sequence to be used
87 for phylogenetic inference. For instance, columns with more than 50% gaps can be deleted, like so:
99 = Phylogenetic Trees =
101 == Reading and Writing of Phylogenetic Trees ==
111 Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
114 == Phylogenetic Inference ==
116 *Currently !BioRuby does not contain any wrappers for phylogenetic inference, I am progress of writing a RAxML wrapper followed by a wrapper for FastMA.*
118 == Maximum Likelihood ==
131 == Pairwise Distance Based Methods ==
144 = Analyzing Phylogenetic Trees =
146 == Gene Duplication Inference ==
148 _need to further test and then import GSoC 'SDI' work..._