| Bio::Tools::Run::Phylo::QuickTree(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Phylo::QuickTree(3pm) |
Bio::Tools::Run::Phylo::QuickTree - Wrapper for rapid
reconstruction of
phylogenies using QuickTree
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);
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;
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
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 of the bugs and their resolution. Bug reports can be submitted via the web:
http://redmine.open-bio.org/projects/bioperl/
Email bix@sendu.me.uk
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 : None
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]
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.
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.
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.
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 compliant object (eg. Bio::SimpleAlign).
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
Title : _writeAlignFile Usage : obj->_writeAlignFile($seq) Function: Internal(not to be used directly) Returns : filename Args : Bio::Align::AlignI
| 2018-09-14 | perl v5.26.2 |