Bio::Tools::Run::Phylo::Njtree::Best

NAME

Bio::Tools::Run::Phylo::Njtree::Best - Wrapper around the Njtree (Njtree/phyml) best program.

SYNOPSIS

use Bio::Tools::Run::Phylo::Njtree::Best;
use Bio::AlignIO;
use Bio::TreeIO;
my $alignio = Bio::AlignIO->new(-format => 'fasta',
-file => 't/data/njtree_aln2.nucl.mfa');
my $aln = $alignio->next_aln;
my $treeio = Bio::TreeIO->new(
-format => 'nhx', -file => 't/data/species_tree_njtree.nh');
my $tree = $treeio->next_tree;
my $njtree_best = Bio::Tools::Run::Phylo::Njtree::Best->new();
$njtree_best->alignment($aln);
$njtree_best->tree($tree);
my $nhx_tree = $njtree_best->run();

DESCRIPTION

This is a wrapper around the best program of Njtree by Li Heng. See http://treesoft.sourceforge.net/njtree.shtml for more information.

Wrapper for the calculation of a reconciled phylogenetic tree with inferred duplication tags from amultiple sequence alignment and a species tree using NJTREE.

Helping the module find your executable
You will need to enable NJTREEDIR to find the njtree program. This can be done in (at least) three ways:

1. Make sure the njtree executable is in your path (i.e.
'which njtree' returns a valid program
2. define an environmental variable NJTREEDIR which points to a
directory containing the 'njtree' app:
In bash
export NJTREEDIR=/home/progs/treesoft/njtree or
In csh/tcsh
setenv NJTREEDIR /home/progs/treesoft/njtree
3. include a definition of an environmental variable NJTREEDIR
in every script that will
BEGIN {$ENV{NJTREEDIR} = '/home/progs/treesoft/njtree'; }
use Bio::Tools::Run::Phylo::Njtree::Best;

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 AT bioperl DOT 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 AT bioperl DOT 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/

AUTHOR - Albert Vilella

Email avilella-at-gmail-dot-com

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 : $factory->program_name()
Function: holds the program name
Returns: string
Args : None

program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :

new
Title : new
Usage : my $njtree_best = Bio::Tools::Run::Phylo::Njtree::Best->new();
Function: Builds a new Bio::Tools::Run::Phylo::Njtree::Best
Returns : Bio::Tools::Run::Phylo::Njtree::Best
Args : -alignment => the Bio::Align::AlignI object
-tree => the Bio::Tree::TreeI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-executable => where the njtree executable resides

See also: Bio::Tree::TreeI, Bio::Align::AlignI

prepare
Title : prepare
Usage : my $rundir = $njtree_best->prepare();
Function: prepare the njtree_best analysis using the default or updated parameters
the alignment parameter and species tree must have been set
Returns : value of rundir
Args : L<Bio::Align::AlignI> object,
L<Bio::Tree::TreeI> object [optional]

run
Title : run
Usage : my $nhx_tree = $njtree_best->run();
Function: run the njtree_best analysis using the default or updated parameters
the alignment parameter must have been set
Returns : L<Bio::Tree::TreeI> object [optional]
Args : L<Bio::Align::AlignI> object
L<Bio::Tree::TreeI> object

error_string
Title : error_string
Usage : $obj->error_string($newval)
Function: Where the output from the last analysus run is stored.
Returns : value of error_string
Args : newvalue (optional)

version
Title : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none

alignment
Title : alignment
Usage : $njtree_best->align($aln);
Function: Get/Set the L<Bio::Align::AlignI> object
Returns : L<Bio::Align::AlignI> object
Args : [optional] L<Bio::Align::AlignI>
Comment : We could potentially add support for running directly on a file
but we shall keep it simple
See also: L<Bio::SimpleAlign>

tree
Title : tree
Usage : $njtree_best->tree($tree, %params);
Function: Get/Set the L<Bio::Tree::TreeI> object
Returns : L<Bio::Tree::TreeI>
Args : [optional] $tree => L<Bio::Tree::TreeI>,
[optional] %parameters => hash of tree-specific parameters
Comment : We could potentially add support for running directly on a file
but we shall keep it simple
See also: L<Bio::Tree::Tree>

check_names
Title : check_names
Usage :
Function:
Example :
Returns :
Args :

_setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for njtree_best program
Example :
Returns : parameter string to be passed to njtree_best
during align or profile_align
Args : name of calling object

Bio::Tools::Run::BaseWrapper methods

save_tempfiles
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)

outfile_name
Title : outfile_name
Usage : my $outfile = $njtree_best->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to

tempdir
Title : tempdir
Usage : my $tmpdir = $self->tempdir();
Function: Retrieve a temporary directory name (which is created)
Returns : string which is the name of the temporary directory
Args : none

cleanup
Title : cleanup
Usage : $njtree_best->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none

io
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none