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 3.5 installed, if you have installed Phylip 3.6 you need to set the environment variable PHYLIPVERSION

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/MailList.shtml - About the mailing lists

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://bugzilla.bioperl.org/ Email jason-at-bioperl.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Tools::Run::Phylo::Phylip::Base(); 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)