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Manual Reference Pages  -  BIO::TOOLS::RUN::PHYLO::PHYLIP::BASE (3)

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NAME

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

CONTENTS

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)



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perl v5.20.3 BIO::TOOLS::RUN::PHYLO::PHYLIP::BASE (3) 2016-04-05

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