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Bio::Tools::Run::Phylo::Phylip::Base(3pm)		User Contributed Perl Documentation		 Bio::Tools::Run::Phylo::Phylip::Base(3pm)

NAME
Bio::Tools::Run::Phylo::Phylip::Base - Base object for Phylip modules 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) perl v5.12.3 2011-06-18 Bio::Tools::Run::Phylo::Phylip::Base(3pm)

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Bio::Tools::Phylo::Phylip::ProtDist(3pm)		User Contributed Perl Documentation		  Bio::Tools::Phylo::Phylip::ProtDist(3pm)

NAME
Bio::Tools::Phylo::Phylip::ProtDist - parser for ProtDist output SYNOPSIS
use Bio::Tools::Phylo::Phylip::ProtDist; my $parser = Bio::Tools::Phylo::Phylip::ProtDist->new(-file => 'outfile'); while( my $result = $parser->next_matrix) { # do something with it } DESCRIPTION
A parser for ProtDist output into a Bio::Matrix::PhylipDist object. See also Bio::Matrix::IO::phylip this module may go away. 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: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Shawn Hoon Email shawnh@fugu-sg.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::Phylo::Phylip::ProtDist->new(); Function: Builds a new Bio::Tools::Phylo::Phylip::ProtDist object Returns : Bio::Tools::ProtDist Args : -fh/-file => $val, # for initing input, see Bio::Root::IO -program => 'programname' # name of the program next_matrix Title : next_matrix Usage : my $matrix = $parser->next_matrix Function: Get the next result set from parser data Returns : L<Bio::Matrix::PhylipDist> Args : none perl v5.14.2 2012-03-02 Bio::Tools::Phylo::Phylip::ProtDist(3pm)
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