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 3.6 installed, if you
       have installed Phylip 3.5 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/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 - Jason Stajich

       Email jason-at-bioperl.org

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 = Bio::Tools::Run::Phylo::Phylip::Base->new();
        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)