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)