Bio::Tools::Run::PiseApplication::msa.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::PiseApplication::msa

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::msa
       Bioperl class for:
 
         MSA     multiple sequence alignment (S. F. Altschul)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/msa.html 
          for available values):
 
 
                 msa (String)
 
                 seqs (Sequence)
                         Sequences File
 
                 optimal (Switch)
                         Turns off the optimal multiple alignment
 
                 forcedres (InFile)
                         forced aligned residues file (see the documentation)
 
                 endgap (Switch)
                         charges terminal gaps the same as internal gaps
 
                 unweight (Switch)
                         cost = unweighted sum
 
                 maxscore (Integer)
                         maximum score of an optimal multiple alignment
 
                 epsilons (InFile)
                         Epsilons file (see the documentation)
 
                 costs (InFile)
                         Costs file (see the documentation)
 
                 quiet (Switch)
                         suppress verbose 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 (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/msa.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

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