/ 
bioperl-run-1.5.2_100
/ Bio::Tools::Run::PiseApplication::modelfromalign

NAME

Bio::Tools::Run::PiseApplication::modelfromalign

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::modelfromalign

      Bioperl class for:

	SAM	modelfromalign - use an existing multiple alignment to create an initial model (R. Hughey, A. Krogh)


      Parameters: 

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


		modelfromalign (String)

		run (String)
			Run name

		alignfile (Sequence)
			Aligned sequences (-alignfile)

		alignment_weights (InFile)
			Sequence weights for alignments used to form initial models (-alignment_weights)

		align_fim (Switch)
			Add FIMs to the ends of the initial model (-align_fim)

		regularizerfile (Excl)
			Regularizer (-regularizerfile)

		reglength (Integer)
			Length of the regularizer (-reglength)

		priorlibrary (Excl)
			Dirichlet mixture prior (-priorlibrary)

		prior_weight (Float)
			Weight of the prior library (-prior_weight)

		del_jump_conf (Float)
			Confidence in the regularizer for transitions leaving a delete state. The regularizer's transition values are multiplied by this number (-del_jump_conf)

		ins_jump_conf (Float)
			Confidence in the regularizer for transitions leaving an insert state (-ins_jump_conf)

		insconf (Float)
			Confidence in the regularizer for character probabilities in an insert state (-insconf)

		match_jump_conf (Float)
			Confidence in the regularizer for transitions leaving a match state (-match_jump_conf)

		matchconf (Float)
			Confidence in the regularizer for character probabilities in a match state (-matchconf)

		mainline_cutoff (Float)
			Confidence in the regularizer for transitions leaving a match state (-mainline_cutoff)

		binary_output (Switch)
			Write models in binary format (-binary_output)

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/modelfromalign.html

  • Bio::Tools::Run::PiseApplication

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

  • Bio::Tools::Run::PiseJob

new

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