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

NAME

Bio::Tools::Run::PiseApplication::dnapars

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::dnapars

      Bioperl class for:

	Phylip	dnapars - DNA Parsimony Program (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/dnapars.html 
         for available values):


		dnapars (String)

		infile (Sequence)
			Alignement File
			pipe: readseq_ok_alig

		use_threshold (Switch)
			Use Threshold parsimony (T)

		threshold (Integer)
			Threshold value (if use threshold parsimony)

		use_transversion (Switch)
			Use Transversion parsimony (N)

		seqboot (Switch)
			Perform a bootstrap before analysis

		method (Excl)
			Resampling methods

		seqboot_seed (Integer)
			Random number seed (must be odd)

		jumble_message (Label)
			(You may also enter a random number seed for jumble)

		replicates (Integer)
			How many replicates

		consense (Switch)
			Compute a consensus tree

		multiple_dataset (String)

		bootconfirm (String)

		bootterminal_type (String)

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

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

		times (Integer)
			Number of times to jumble

		user_tree (Switch)
			Use User tree (default: no, search for best tree) (U)

		tree_file (InFile)
			User Tree file

		weights (Switch)
			Use weights for sites (W)

		weights_file (InFile)
			Weights file
			pipe: phylip_weights

		print_tree (Switch)
			Print out tree (3)

		print_steps (Switch)
			Print out steps in each site (4)

		print_sequences (Switch)
			Print sequences at all nodes of tree (5)

		print_treefile (Switch)
			Write out trees onto tree file (6)

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

		indent_tree (Switch)
			Indent treefile

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

		confirm (String)

		terminal_type (String)

		consense_confirm (String)

		consense_terminal_type (String)

		consense_outgroup (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/dnapars.html

  • Bio::Tools::Run::PiseApplication

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

  • Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $dnapars = Bio::Tools::Run::PiseApplication::dnapars->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::dnapars 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 $dnapars = $factory->program('dnapars');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::dnapars.