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Bio::Tools::Run::PhyloUserBContributed Perl DocuBio::Tools::Run::Phylo::LVB(3) NAME Bio::Tools::Run::Phylo::LVB - Object for using the LVB program to create an array of Bio::Tree objects from a nucleotide multiple alignment file or a nucleotide SimpleAlign object. Works with LVB version 2.1. SYNOPSIS use Bio::Tools::Run::Phylo::LVB; # Create a SimpleAlign object. # NOTE. Aligning nucleotide sequence directly, as below, makes # sense for non-coding nucleotide sequence (e.g., structural RNA # genes, introns, ITS). For protein-coding genes, to prevent # Clustal intronducing frameshifts one should instead align the # translations of the genes, then convert the multiple alignment # to nucleotide by referring to the corresponding transcript # sequences (e.g., using EMBOSS tranalign). use Bio::Tools::Run::Alignment::Clustalw; $aln_factory = Bio::Tools::Run::Alignment::Clustalw->new(quiet => 1); $inputfilename = "/Users/daniel/nuc.fa"; $aln = $aln_factory->align($inputfilename); # Create the tree or trees. $tree_factory = Bio::Tools::Run::Phylo::LVB->new(quiet => 1); @trees = $tree_factory->run($aln); # Or one can pass in a file name containing a nucleotide multiple # alignment in Phylip 3.6 format: $tree_factory = Bio::Tools::Run::Phylo::LVB->new(quiet => 1); $tree = $tree_factory->run("/Users/daniel/nuc.phy"); DESCRIPTION Wrapper for LVB, which uses a simulated annealing heuristic search to seek parsimonious trees from a nucleotide multiple alignment. FEEDBACK Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: http://redmine.open-bio.org/projects/bioperl/ PARAMETERS FOR LVB COMPUTATION FORMAT Title : FORMAT Description : (optional) When running LVB from a Phylip 3.6-format multiple alignment file, this specifies the layout of the file. It may be "interleaved" or "sequential". FORMAT is automatically set to "interleaved" if running from a SimpleAlign object. Defaults to "interleaved". GAPS Title : GAPS Description : (optional) LVB can treat gaps represented in the multiple alignment by "-" as either "fifthstate" or "unknown". "fifthstate" regards "-" as equivalent to "O", which is an unambiguous character state distinct from all nucleotides. "unknown" regards "-" as equivalent to "?", which is as an ambiguous site that may contain "A" or "C" or "G" or "T" or "O". Defaults to "unknown". SEED Title : SEED Description : (optional) This specifies the random number seed for LVB. SEED must be an integer in the range 0 to 900000000 inclusive. If no seed is specified, LVB takes a seed from the system clock. By default, no seed is specified. DURATION Title : DURATION Description : (optional) This specifies the duration of the analysis, which may be "fast" or "slow". "slow" causes LVB to perform a more thorough and more time-consuming search than "fast". Defaults to "slow". BOOTSTRAPS Title : BOOTSTRAPS Description : (optional) This specifies the number of bootstrap replicates to use, which must be a positive integer. Set bootstraps to 0 for no bootstrapping. Defaults to 0. AUTHOR Daniel Barker CONTRIBUTORS Email jason-AT-bioperl_DOT_org APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ program_name Title : program_name Usage : ->program_name() Function: holds the program name Returns: string Args : None program_dir Title : program_dir Usage : ->program_dir() Function: returns undef Args : run Title : run Usage : $inputfilename = '/Users/daniel/nuc.phy'; @trees = $factory->run($inputfilename); Function: Create one or more LVB trees from a SimpleAlign object or a file containing a Phylip 3.6-format nucleotide multiple alignment. Example : Returns : Array of L<Bio::Tree> objects Args : Name of a file containing a nucleotide multiple alignment in Phylip 3.6 format, or a SimpleAlign object create_tree Title : create_tree Usage : $inputfilename = '/Users/daniel/nuc.phy'; @trees = $factory->create_tree($inputfilename); Function: Create one or more LVB trees from a SimpleAlign object or a file containing a Phylip 3.6-format nucleotide multiple alignment. Example : Returns : Array of L<Bio::Tree> objects Args : Name of a file containing a nucleotide multiple alignment in Phylip 3.6 format, or a SimpleAlign object _run Title : _run Usage : Internal function, not to be called directly Function: makes actual system call to lvb program Example : Returns : Array of Bio::Tree objects Args : Name of a file containing a multiple alignment in Phylip 3.6 format and a parameter string to be passed to LVB _setinput Title : _setinput Usage : Internal function, not to be called directly Function: Create input file for lvb program Example : Returns : name of file containing a multiple alignment in Phylip 3.6 format Args : SimpleAlign object reference or input file name _setparams Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for lvb program Example : Returns : parameter string to be passed to LVB Args : name of calling object perl v5.32.1 2021-03-01 Bio::Tools::Run::Phylo::LVB(3)
NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | PARAMETERS FOR LVB COMPUTATION | AUTHOR | CONTRIBUTORS | APPENDIX
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