Bio::Tools::Run::PiseApplication::modelfromalign(3)

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/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/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.