/ 
bioperl-run-1.4
/ Bio::Tools::Run::PiseApplication::neighbor

NAME

Bio::Tools::Run::PiseApplication::neighbor

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::neighbor

      Bioperl class for:

	Phylip	neighbor - Neighbor-Joining and UPGMA methods (Felsenstein)

	References:

		Felsenstein, J.  1993.  PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author.  Department of Genetics, University of Washington, Seattle.

		Felsenstein, J.  1989.  PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics  5: 164-166.



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/neighbor.html 
         for available values):


		neighbor (String)

		distance_method (Excl)
			Distance method

		infile (InFile)
			Distances matrix File
			pipe: phylip_dist

		jumble (Switch)
			Randomize (jumble) input order (J)

		jumble_seed (Integer)
			Random number seed for jumble (must be odd)

		multiple_dataset (Switch)
			Analyze multiple data sets (M)

		datasets_nb (Integer)
			How many data sets

		multiple_seed (Integer)
			Random number seed for multiple dataset (must be odd)

		consense (Switch)
			Compute a consensus tree

		consense_confirm (String)

		consense_terminal_type (String)

		print_tree (Switch)
			Print out tree (3)

		print_treefile (Switch)
			Write out trees onto tree file (4)

		indent_tree (Switch)
			Indent treefile

		printdata (Switch)
			Print out the data at start of run (1)

		outgroup (Integer)
			Outgroup species (default, use as outgroup species 1) (O)

		triangular (Excl)
			Matrix format

		confirm (String)

		terminal_type (String)

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/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 email or the web:

bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

  • http://bioweb.pasteur.fr/seqanal/interfaces/neighbor.html

  • Bio::Tools::Run::PiseApplication

  • Bio::Tools::Run::AnalysisFactory::Pise

  • Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $neighbor = Bio::Tools::Run::PiseApplication::neighbor->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::neighbor object.
          This method should not be used directly, but rather by 
          a Bio::Tools::Run::AnalysisFactory::Pise instance.
          my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
          my $neighbor = $factory->program('neighbor');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::neighbor.