Provided by: libbio-perl-run-perl_1.7.1-3_all bug


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


       # Do not use directly # This module is for setting basic data sets for the Phylip wrapper
       # modules


       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


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AUTHOR - Jason Stajich



       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        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    :

        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
        Returns : value of outfile
        Args    : newvalue (optional)

        Title   : treefile
        Usage   : $obj->treefile($newval)
        Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
        Returns : value of treefile
        Args    : newvalue (optional)

        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)

        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)

        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)