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

NAME

Bio::Tools::Run::PiseApplication::dnadist

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::dnadist

      Bioperl class for:

	Phylip	dnadist - Compute distance matrix from nucleotide sequences (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/dnadist.html 
         for available values):


		dnadist (String)

		infile (Sequence)
			Alignment File
			pipe: readseq_ok_alig

		distance (Excl)
			Distance (D)

		ratio (Integer)
			Transition/transversion ratio (T)

		gamma (Excl)
			Gamma distributed rates across sites (G)

		variation_coeff (Float)
			Coefficient of variation of substitution rate among sites (must be positive) (if Gamma)

		invariant_sites (Float)
			Fraction of invariant sites (if Gamma)

		empirical_frequencies (Switch)
			Use empirical base frequencies (F)

		base_frequencies (String)
			Base frequencies for A, C, G, T/U (if not empirical) (separated by commas)

		one_category (Switch)
			One category of substitution rates (C)

		n_categ (Integer)
			Number of categories (1 to 9)

		categ_rates (String)
			Rate for each category (separated by commas)

		weights (Switch)
			Use weights for sites (W)

		weights_file (InFile)
			Weights file

		seqboot (Switch)
			Perform a bootstrap before analysis

		method (Excl)
			Resampling methods

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

		replicates (Integer)
			How many replicates

		matrix_form (Switch)
			Lower-triangular distance matrix (L)

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

		confirm (String)

		terminal_type (String)

		multiple_dataset (String)

		seqboot_confirm (String)

		seqboot_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/dnadist.html

  • Bio::Tools::Run::PiseApplication

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

  • Bio::Tools::Run::PiseJob

new

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