Bio::Tools::Run::PiseApplication::emma # 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)

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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.bioperl.org/ 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. This software is provided "as is" without warranty of any kind. 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.