/ 
bioperl-run-1.5.2_005-RC
/ Bio::Tools::Run::Phylo::LVB

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

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.open-bio.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-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