Bio::Tools::Run::PiseApplication::emma.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::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/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/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.