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. 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"); Wrapper for LVB, which uses a simulated annealing heuristic search to seek parsimonious trees from a nucleotide multiple alignment.

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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. Daniel Barker Email jason@bioperl.org 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