Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::Tools::Run::Phylo::LVB.3pm

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://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