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.
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");
Wrapper for LVB, which uses a simulated annealing heuristic search to seek parsimonious trees from a nucleotide multiple alignment.
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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".
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".
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.
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".
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.
Daniel Barker
Email jason-AT-bioperl_DOT_org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : ->program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : ->program_dir() Function: returns undef Args :
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
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
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
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
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