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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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)