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

NAME
Bio::Tools::Run::PiseApplication::emma

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::emma

      Bioperl class for:

        EMMA    Multiple alignment program - interface to ClustalW program (EMBOSS)

      Parameters:

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

                emma (String)

                init (String)

                inseqs (Sequence)
                        inseqs -- gapany [sequences] (-inseqs)
                        pipe: seqsfile

                onlydend (Switch)
                        Do you want to produce only the dendrogram file? (-onlydend)

                dend (Switch)
                        Do you want to use an old dendogram file? (-dend)

                dendfile (String)
                        What is the name of the old dendrogram file (-dendfile)

                insist (Switch)
                        Insist that the sequence type is changed to protein (-insist)

                slowfast (Excl)
                        Please select one -- Do you want to carry out slow or fast pairwise alignment (-slowfast)

                pwgapc (Float)
                        Input value for gap open penalty (-pwgapc)

                pwgapv (Float)
                        Input value for gap extension penalty (-pwgapv)

                prot (Switch)
                        Do not change this value (-prot)

                pwmatrix (Excl)
                        Select matrix -- Protein pairwise alignment matrix options (-pwmatrix)

                pwdnamatrix (Excl)
                        Select matrix -- DNA pairwise alignment matrix options (-pwdnamatrix)

                pairwisedata (String)
                        Input the filename of your pairwise matrix (-pairwisedata)

                ktup (Integer)
                        Fast pairwise alignment: similarity scores: K-Tuple size (-ktup)

                gapw (Integer)
                        Fast pairwise alignment: similarity scores: gap penalty (-gapw)

                topdiags (Integer)
                        Fast pairwise alignment: similarity scores: number of diagonals to be considered (-topdiags)

                window (Integer)
                        Fast pairwise alignment: similarity scores: diagonal window size (-window)

                nopercent (Switch)
                        Fast pairwise alignment: similarity scores: suppresses percentage score (-nopercent)

                matrix (Excl)
                        Select matrix -- Protein multiple alignment matrix options (-matrix)

                dnamatrix (Excl)
                        Select matrix -- Nucleotide multiple alignment matrix options (-dnamatrix)

                mamatrix (String)
                        Input the filename of your alignment matrix (-mamatrix)

                gapc (Float)
                        Enter gap penalty (-gapc)

                gapv (Float)
                        Enter variable gap penalty (-gapv)

                endgaps (Switch)
                        Use end gap separation penalty (-endgaps)

                gapdist (Integer)
                        Gap separation distance (-gapdist)

                norgap (Switch)
                        No residue specific gaps (-norgap)

                hgapres (String)
                        List of hydrophilic residues (-hgapres)

                nohgap (Switch)
                        No hydrophilic gaps (-nohgap)

                maxdiv (Integer)
                        Cut-off to delay the alignment of the most divergent sequences (-maxdiv)

                outseq (OutFile)
                        The sequence alignment output filename (-outseq)
                        pipe: seqsfile

                outseq_sformat (Excl)
                        Output format for: The sequence alignment output filename

                dendoutfile (OutFile)
                        The dendogram output filename (-dendoutfile)

                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/emma.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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