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

NAME
Bio::Tools::Run::PiseApplication::infoalign

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::infoalign

      Bioperl class for:

        INFOALIGN       Information on a multiple sequence alignment (EMBOSS)

      Parameters:

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

                infoalign (String)

                init (String)

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

                refseq (String)
                        The number or the name of the reference sequence (-refseq)

                matrix (Excl)
                        Similarity scoring Matrix file (-matrix)

                plurality (Float)
                        Plurality check % for consensus (-plurality)

                identity (Float)
                        Required % of identities at a position fro consensus (-identity)

                outfile (OutFile)
                        Output sequence details to a file (-outfile)

                html (Switch)
                        Format output as an HTML table (-html)

                only (Switch)
                        Display the specified columns (-only)

                heading (Switch)
                        Display column headings (-heading)

                usa (Switch)
                        Display the USA of the sequence (-usa)

                name (Switch)
                        Display 'name' column (-name)

                seqlength (Switch)
                        Display 'seqlength' column (-seqlength)

                alignlength (Switch)
                        Display 'alignlength' column (-alignlength)

                gaps (Switch)
                        Display number of gaps (-gaps)

                gapcount (Switch)
                        Display number of gap positions (-gapcount)

                idcount (Switch)
                        Display number of identical positions (-idcount)

                simcount (Switch)
                        Display number of similar positions (-simcount)

                diffcount (Switch)
                        Display number of different positions (-diffcount)

                change (Switch)
                        Display % number of changed positions (-change)

                description (Switch)
                        Display 'description' column (-description)

                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/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/infoalign.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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