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                  the phylip package.

=head2 OUTGROUP (*ONLY AVAILABLE FOR NEIGHBOR JOINING)

  Title		: OUTGROUP 
  Description	: (optional)
                  This option selects the species to be used as the outgroup
  Acceptable Values: integer 
  Usage         : @params = ('outgroup'=>'X'); 
                  where X is an positive integer not more than the 
                  number of sequences 
		  Defaults to 1

=head2 LOWTRI

  Title		: LOWTRI
  Description   : (optional)
                  This indicates that the distance matrix is 
                  input  in  Lower-triangular form  (the  lower-left 
		  half of the distance matrix only, without the zero 
		  diagonal elements)
  Usage         : @params = ('lowtri'=>'X'); where X is either 1 or 0 
		  Defaults to 0 

=head2 UPPTRI

  Title         : UPPTRI 
  Description   : (optional)
                  This indicates that the distance matrix is input  in  
                  upper-triangular form  (the  upper-right half of the 
		  distance matrix only, without the zero diagonal elements.)
Usage           : @params = ('upptri'=>'X'); where X is either 1 or 0 
                  Defaults to 0 

=head2 SUBREP

  Title         : SUBREP 
  Description   : (optional)
                  This is the Subreplication option.  

		  It informs the program that after each distance will
		  be provided an integer indicating that the distance
		  is a mean of that many replicates.

  Usage         : @params = ('subrep'=>'X'); where X is either 1 or 0 
                  Defaults to 0 

=head2 JUMBLE

  Title        : JUMBLE 
  Description  : (optional)

                 This enables you to tell the program to use a random
                 number generator to choose the input order of
                 species.  seed: an integer between 1 and 32767 and of
                 the form 4n+1 which means that it must give a
                 remainder of 1 when divided by 4.  Each different
                 seed leads to a different sequence of addition of
                 species.  By simply changing the random number seed
                 and re-running programs one can look for other, and
                 better trees.  iterations:

  Usage        : @params = ('jumble'=>'17); where 17 is the random seed
                 Defaults to no jumble

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<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.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:

  http://redmine.open-bio.org/projects/bioperl/

=head1 AUTHOR - Shawn Hoon 

Email shawnh@fugu-sg.org 

=head1 CONTRIBUTORS

Email:jason-at-bioperl.org

=head1 APPENDIX

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

=cut

#'

	
package Bio::Tools::Run::Phylo::Phylip::Neighbor;

use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
	    @NEIGHBOR_PARAMS @OTHER_SWITCHES
	    %OK_FIELD);
use strict;
use Bio::SimpleAlign;
use Bio::AlignIO;