NAME

Bio::Tools::Run::PiseApplication::distmat

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::distmat

      Bioperl class for:

	DISTMAT	Creates a distance matrix from multiple alignments (EMBOSS)


      Parameters: 

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


		distmat (String)

		init (String)

		msf (Sequence)
			msf -- gapany [set of sequences] (-msf)
			pipe: seqsfile

		nucmethod (Excl)
			Method to use -- Multiple substitution correction methods for nucleotides (-nucmethod)

		protmethod (Excl)
			Method to use -- Multiple substitution correction methods for proteins (-protmethod)

		ambiguous (Switch)
			Use the abiguous codes in the calculation. (-ambiguous)

		gapweight (Float)
			Weight given to gaps (-gapweight)

		position (Integer)
			Base position to analyse. (-position)

		calculatea (Switch)
			Calculate the a-parameter (-calculatea)

		parametera (Float)
			a-parameter (-parametera)

		outf (OutFile)
			Enter a name for the distance matrix (-outf)

		auto (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/wiki/Mailing_lists  - 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 the web:

http://bugzilla.open-bio.org/

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/distmat.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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