Bio::Tools::Run::PhyloUseriContributed PerBio::Tools::Run::Phylo::QuickTree(3)NAMEBio::Tools::Run::Phylo::QuickTree - Wrapper for rapid reconstruction of
phylogenies using QuickTree
SYNOPSIS
use Bio::Tools::Run::Phylo::QuickTree;
# Make a QuickTree factory
@params = ();
$factory = Bio::Tools::Run::Phylo::QuickTree->new(@params);
# Pass the factory an alignment
$inputfilename = 't/data/cysprot.stockholm';
$tree = $factory->run($inputfilename); # $tree is a Bio::Tree::Tree object.
# or get a Bio::Align::AlignI (SimpleAlign) object from somewhere
$tree = $factory->run($aln);
DESCRIPTION
This is a wrapper for running the QuickTree application by Kevin Howe.
You can download it here:
http://www.sanger.ac.uk/Software/analysis/quicktree/
Currently only input with alignments and output of trees is supported.
(Ie. no support for distance matrix in/out.)
You will need to enable this QuickTree wrapper to find the quicktree
program. This can be done in (at least) three ways:
1. Make sure the QuickTree executable is in your path.
2. Define an environmental variable QUICKTREEDIR which is a
directory which contains the 'quicktree' application:
In bash:
export QUICKTREEDIR=/home/username/quicktree_1.1/bin
In csh/tcsh:
setenv QUICKTREEDIR /home/username/quicktree_1.1/bin
3. Include a definition of an environmental variable QUICKTREEDIR in
every script that will use this QuickTree wrapper module, e.g.:
BEGIN { $ENV{QUICKTREEDIR} = '/home/username/quicktree_1.1/bin' }
use Bio::Tools::Run::Phylo::QuickTree;
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 the
Bioperl mailing list. 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 of
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
AUTHOR - Sendu Bala
Email bix@sendu.me.uk
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 : None
new
Title : new
Usage : $factory = Bio::Tools::Run::Phylo::QuickTree->new(@params)
Function: creates a new QuickTree factory
Returns : Bio::Tools::Run::Phylo::QuickTree
Args : Optionally, provide any of the following (default in []):
-upgma => boolean # Use the UPGMA method to construct the tree [0]
-kimura => boolean # Use the kimura translation for pairwise
# distances [0]
-boot => int # Calculate bootstrap values with n iterations [0]
upgma
Title : upgma
Usage : $factory->upgma(1);
Function: Choose to use the UPGMA method to construct the tree.
Returns : boolean (default 0)
Args : None to get, boolean to set.
kimura
Title : kimura
Usage : $factory->kimura(1);
Function: Choose to use the kimura translation for pairwise distances.
Returns : boolean (default 0)
Args : None to get, boolean to set.
boot
Title : boot
Usage : $factory->boot(100);
Function: Choose to calculate bootstrap values with the supplied number of
iterations.
Returns : int (default 0)
Args : None to get, int to set.
run
Title : run
Usage : $factory->run($stockholm_file);
$factory->run($align_object);
Function: Runs QuickTree to generate a tree
Returns : Bio::Tree::Tree object
Args : file name for your input alignment in stockholm format, OR
Bio::Align::AlignI complient object (eg. Bio::SimpleAlign).
_setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: Creates a string of params to be used in the command string
Returns : string of params
Args : none
_writeAlignFile
Title : _writeAlignFile
Usage : obj->_writeAlignFile($seq)
Function: Internal(not to be used directly)
Returns : filename
Args : Bio::Align::AlignI
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