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

NAME
Bio::Tools::Run::PiseApplication::clustalw

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::clustalw

      Bioperl class for:

        Clustalw        Multiple Alignments (Des Higgins)

        References:

                Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22:4673-4680.

      Parameters:

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

                clustalw (String)

                infile (Sequence)
                        Sequences File  (or Alignment File for Bootstrap and Tree actions) (-infile)
                        pipe: seqsfile
                        pipe: readseq_ok_alig

                actions (Excl)
                        Actions

                phylip_alig (Switch)
                        Phylip alignment output format (-output)

                quicktree (Excl)
                        Toggle Slow/Fast pairwise alignments (-quicktree)

                typeseq (Excl)
                        Protein or DNA (-type)

                matrix (Excl)
                        Protein weight matrix (-matrix)

                dnamatrix (Excl)
                        DNA weight matrix (-dnamatrix)

                gapopen (Integer)
                        Gap opening penalty (-gapopen)

                gapext (Float)
                        Gap extension penalty (-gapext)

                endgaps (Switch)
                        End gap separation penalty (-endgaps)

                gapdist (Integer)
                        Gap separation pen. range (-gapdist)

                pgap (Switch)
                        Residue specific penalties (Pascarella gaps) (-nopgap)

                hgap (Switch)
                        Hydrophilic gaps (-nohgap)

                hgapresidues (List)
                        Hydrophilic residues list (-hgapresidues)

                maxdiv (Integer)
                        Delay divergent sequences : % ident. for delay (-maxdiv)

                negative (Switch)
                        Negative values in matrix ? (-negative)

                transweight (Float)
                        Transitions weight (between 0 and 1) (-transweight)

                newtree (OutFile)
                        File for new guide tree (-newtree)

                usetree (InFile)
                        File for old guide tree (-usetree)

                ktuple (Integer)
                        Word size (-ktuple)

                topdiags (Integer)
                        Number of best diagonals (-topdiags)

                window (Integer)
                        Window around best diags (-window)

                pairgap (Float)
                        Gap penalty (-pairgap)

                score (Excl)
                        Percent or absolute score ? (-score)

                pwmatrix (Excl)
                        Protein weight matrix (-pwmatrix)

                pwdnamatrix (Excl)
                        DNA weight matrix (-pwdnamatrix)

                pwgapopen (Float)
                        Gap opening penalty (-pwgapopen)

                pwgapext (Float)
                        Gap extension penalty (-pwgapext)

                kimura (Switch)
                        Use Kimura's correction (multiple substitutions) ? (-kimura)

                tossgaps (Switch)
                        Ignore positions with gaps ? (-tossgaps)

                bootstrap (Integer)
                        Bootstrap a NJ tree (give the number of bootstraps, 0 for none) (-bootstrap)

                bootlabels (Excl)
                        Phylip bootstrap positions (-bootlabels)

                seed (Integer)
                        Seed number for bootstraps (-seed)

                outputtree (Excl)
                        Output tree/distance format (-outputtree)

                outfile (OutFile)
                        Alignment File (-outfile)
                        pipe: readseq_ok_alig

                output (Excl)
                        Output format (-output)

                gde_lower (Switch)
                        Upper case GDE output (-case)

                outorder (Excl)
                        Result order (-outorder)

                seqnos (Switch)
                        Output sequence numbers in the output file (clustalw format) (-seqnos)

                profile1 (InFile)
                        Profile 1 (-profile1)

                profile2 (InFile)
                        Profile 2 (-profile2)

                usetree1 (InFile)
                        File for old guide tree for profile1 (-usetree1)

                usetree2 (InFile)
                        File for old guide tree for profile2 (-usetree2)

                newtree1 (OutFile)
                        File for new guide tree for profile1 (-newtree1)

                newtree2 (OutFile)
                        File for new guide tree for profile2 (-newtree2)

                nosecstr1 (Switch)
                        Use profile 1 secondary structure / penalty mask (-nosecstr1)

                nosecstr2 (Switch)
                        Use profile 2 secondary structure / penalty mask (-nosecstr2)

                helixgap (Integer)
                        Helix gap penalty (-helixgap)

                strandgap (Integer)
                        Strand gap penalty (-strandgap)

                loopgap (Integer)
                        Loop gap penalty (-loopgap)

                terminalgap (Integer)
                        Secondary structure terminal penalty (-terminalgap)

                helixendin (Integer)
                        Helix terminal positions:  number of residues inside helix to be treated as terminal (-helixendin)

                helixendout (Integer)
                        Helix terminal positions: number of residues outside helix to be treated as terminal (-helixendout)

                strandendin (Integer)
                        Strand terminal positions: number of residues inside strand to be treated as terminal (-strandendin)

                strandendout (Integer)
                        Strand terminal positions: number of residues outside strand to be treated as terminal (-strandendout)

                secstrout (Excl)
                        Output in alignment (-secstrout)

FEEDBACK
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
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.bioperl.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/clustalw.html

•   Bio::Tools::Run::PiseApplication

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

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