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Bio::Tools::Run::Phylo::QuickTree.3pm

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://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