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.IX Title "Bio::Tools::Run::Phylo::Phylip::Base 3pm"
.TH Bio::Tools::Run::Phylo::Phylip::Base 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::Phylo::Phylip::Base \- Base object for Phylip modules
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
# Do not use directly
# This module is for setting basic data sets for the Phylip wrapper
# modules
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This module is just a base object for Bioperl Phylip wrappers.
.PP
\&\s-1IMPORTANT PHYLIP VERSION ISSUES\s0
By default we assume you have Phylip 3.6 installed, if you
have installed Phylip 3.5 you need to set the environment variable
\&\s-1PHYLIPVERSION\s0
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason\-at\-bioperl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 5
\& 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    :
.Ve
.SS "outfile"
.IX Subsection "outfile"
.Vb 9
\& Title   : outfile
\& Usage   : $obj\->outfile($newval)
\& Function: Get/Set default PHYLIP outfile name (\*(Aqoutfile\*(Aq usually)
\&           Changing this is only necessary when you have compiled
\&           PHYLIP to use a different filename for the default \*(Aqoutfile\*(Aq
\&           This will not change the default output filename by 
\&           PHYLIP
\& Returns : value of outfile
\& Args    : newvalue (optional)
.Ve
.SS "treefile"
.IX Subsection "treefile"
.Vb 5
\& Title   : treefile
\& Usage   : $obj\->treefile($newval)
\& Function: Get/Set the default PHYLIP treefile name (\*(Aqtreefile\*(Aq usually)
\& Returns : value of treefile
\& Args    : newvalue (optional)
.Ve
.SS "fontfile"
.IX Subsection "fontfile"
.Vb 5
\& 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)
.Ve
.SS "plotfile"
.IX Subsection "plotfile"
.Vb 5
\& 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)
.Ve
.SS "version"
.IX Subsection "version"
.Vb 5
\& 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)
.Ve