Bio::Tools::Run::Phylo::Phylip::Base(3)

NAME
Bio::Tools::Run::Phylo::Phylip::Base - Base object for Phylip modules

SYNOPSIS
# Do not use directly # This module is for setting basic data sets for the Phylip wrapper # modules

DESCRIPTION
This module is just a base object for Bioperl Phylip wrappers.

IMPORTANT PHYLIP VERSION ISSUES By default we assume you have Phylip 3.5 installed, if you have installed Phylip 3.6 you need to set the environment variable PHYLIPVERSION

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/MailList.shtml  - About the mailing lists

  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 email or the web:

  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/bioperl-bugs/

AUTHOR - Jason Stajich
Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS
Additional contributors names and emails here

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  new
 Title   : new
 Usage   : my $obj = new Bio::Tools::Run::Phylo::Phylip::Base();
 Function: Builds a new Bio::Tools::Run::Phylo::Phylip::Base object
 Returns : an instance of Bio::Tools::Run::Phylo::Phylip::Base
 Args    :

  outfile
 Title   : outfile
 Usage   : $obj->outfile($newval)
 Function: Get/Set default PHYLIP outfile name ('outfile' usually)
           Changing this is only necessary when you have compiled
           PHYLIP to use a different filename for the default 'outfile'
           This will not change the default output filename by
           PHYLIP
 Returns : value of outfile
 Args    : newvalue (optional)

  treefile
 Title   : treefile
 Usage   : $obj->treefile($newval)
 Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
 Returns : value of treefile
 Args    : newvalue (optional)

  fontfile
 Title   : fontfile
 Usage   : $obj->fontfile($newval)
 Function: Get/Set the fontfile
 Returns : value of fontfile (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

  plotfile
 Title   : plotfile
 Usage   : $obj->plotfile($newval)
 Function: Get/Set the plotfile
 Returns : value of plotfile (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

  version
 Title   : version
 Usage   : $obj->version($newval)
 Function: Get/Set the version
 Returns : value of version (a scalar)
 Args    : on set, new value (a scalar or undef, optional)