Bio::Tools::Run::PiseApplication::combat # Bio::Tools::Run::PiseApplication::combat Bioperl class for: COMBAT Comparison of coding DNA (Pedersen, Lyngso,Hein) References: Christian N. S. Pedersen, Rune B. Lyngso and Jotun Hein. Comparison of coding DNA in Proceedings of the 9th Annual Symposium of Combinatorial Pattern Matching (CPM), 1998. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/combat.html for available values): combat (String) sequence1 (Sequence) First Sequence sequence2 (Sequence) Second Sequence output_aln (OutFile) alignment_file (OutFile) pipe: readseq_ok_alig protein_distance_matrix (Excl) Amino-acid distance matrix nucleotide_distance_matrix (Excl) Nucleotid distance matrix protein_gap_open (Integer) Gap open cost for protein protein_gap_ext (Integer) Gap extension cost for protein dna_gap_open (Integer) Gap open cost for dna dna_gap_ext (Integer) Gap extension cost for dna gnuplot_call (String) gnuplot_commands (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/combat.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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