Bio::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://bio.perl.org/MailList.html   - About the mailing lists

  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://bugzilla.bioperl.org/

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@bioperl.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