/ 
BioPerl-Run-1.007003
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Phylo::Phylip::Base

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)