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 listsSupport
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 : Noneprogram_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
objectcreate_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