| Bio::Tools::Run::Phylo::Njtree::Best(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Phylo::Njtree::Best(3pm) |
Bio::Tools::Run::Phylo::Njtree::Best - Wrapper around the Njtree (Njtree/phyml) best program.
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 = $njtree_best->run();
This is a wrapper around the best program of Njtree by Li Heng. See http://treesoft.sourceforge.net/njtree.shtml for more information.
Wrapper for the calculation of a reconciled phylogenetic tree with inferred duplication tags from amultiple sequence alignment and a species tree using NJTREE.
You will need to enable NJTREEDIR to find the njtree program. This can be done in (at least) three ways:
1. Make sure the njtree executable is in your path (i.e.
'which njtree' returns a valid program
2. define an environmental variable NJTREEDIR which points to a
directory containing the 'njtree' app:
In bash
export NJTREEDIR=/home/progs/treesoft/njtree or
In csh/tcsh
setenv NJTREEDIR /home/progs/treesoft/njtree
3. include a definition of an environmental variable NJTREEDIR
in every script that will
BEGIN {$ENV{NJTREEDIR} = '/home/progs/treesoft/njtree'; }
use Bio::Tools::Run::Phylo::Njtree::Best;
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
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.
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/
Email avilella-at-gmail-dot-com
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $factory->program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args :
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
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]
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
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)
Title : version Usage : exit if $prog->version() < 1.8 Function: Determine the version number of the program Example : Returns : float or undef Args : none
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>
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>
Title : check_names Usage : Function: Example : Returns : Args :
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
Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional)
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
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
Title : cleanup Usage : $njtree_best->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none
Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<Bio::Root::IO> Args : none
| 2023-01-22 | perl v5.36.0 |