NAME

Bio::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://redmine.open-bio.org/projects/bioperl/

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 compliant 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

cpanm Bio::DB::ESoap

perl -MCPAN -e shell
install Bio::DB::ESoap