Bio::Tools::Run::PiseApplication::comalign # Bio::Tools::Run::PiseApplication::comalign Bioperl class for: ComAlign Combining many multiple alignments in one improved alignment (O. Caprani, K. Bucka-Lassen) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/comalign.html for available values): comalign (String) seq (Sequence) Sequences File (-f) pipe: seqsfile seed (Integer) Random seed number (-s) seqnb (Integer) Number of sequences that are to be aligned (-n) iterations (Integer) Number of iterations (-i) score (Integer) score: ComAlign records the time it took to find a solution as good as this score (-l) time (Integer) ComAlign marks the best solution found after this number of 1/100 seconds (-t) last_iterations (Integer) Makes ComAlign terminate if the score hasn't changed within the last this number of iterations (-c) print_best (Switch) Print the best found alignment on termination (-a)

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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/comalign.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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