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Bio::Tools::Run::PhyloUserBContributed Perl DocuBio::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://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

perl v5.24.1			  2017-07-08	Bio::Tools::Run::Phylo::LVB(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | PARAMETERS FOR LVB COMPUTATION | AUTHOR | CONTRIBUTORS | APPENDIX

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