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 Alignments 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 }
70 # Calculates the alignment using the Muscle program on the local
71 # machine with options '-quiet -maxiters 64'
72 # and stores the result in 'report'.
73 options = ['-quiet', '-maxiters', '64']
74 muscle = Bio::Muscle.new('path/to/muscle', options)
75 report = muscle.query_align( seqs)
77 # Accesses the actual alignment
78 align = report.alignment
80 # Prints each sequence to the console.
81 report.align.each { |s| puts s.to_s }
86 == Manipulating Multiple Sequence Alignments ==
88 It is probably a good idea to 'clean up' multiple sequence to be used
89 for phylogenetic inference. For instance, columns with more than 50% gaps can be deleted, like so:
101 = Phylogenetic Trees =
103 == Phylogenetic Tree Input and Output ==
105 === Reading in of Phylogenetic Trees ===
115 Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
117 === Writing of Phylogenetic Trees ===
127 Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
130 == Phylogenetic Inference ==
132 *Currently !BioRuby does not contain any wrappers for phylogenetic inference, I am progress of writing a RAxML wrapper followed by a wrapper for FastMA.*
134 == Maximum Likelihood ==
147 == Pairwise Distance Based Methods ==
160 = Analyzing Phylogenetic Trees =
162 == Gene Duplication Inference ==
164 _need to further test and then import GSoC 'SDI' work..._