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