Bio::Tools::Run::PiseApplication::modelfromalign # Bio::Tools::Run::PiseApplication::modelfromalign Bioperl class for: SAM modelfromalign - use an existing multiple alignment to create an initial model (R. Hughey, A. Krogh) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/modelfromalign.html for available values): modelfromalign (String) run (String) Run name alignfile (Sequence) Aligned sequences (-alignfile) alignment_weights (InFile) Sequence weights for alignments used to form initial models (-alignment_weights) align_fim (Switch) Add FIMs to the ends of the initial model (-align_fim) regularizerfile (Excl) Regularizer (-regularizerfile) reglength (Integer) Length of the regularizer (-reglength) priorlibrary (Excl) Dirichlet mixture prior (-priorlibrary) prior_weight (Float) Weight of the prior library (-prior_weight) del_jump_conf (Float) Confidence in the regularizer for transitions leaving a delete state. The regularizer's transition values are multiplied by this number (-del_jump_conf) ins_jump_conf (Float) Confidence in the regularizer for transitions leaving an insert state (-ins_jump_conf) insconf (Float) Confidence in the regularizer for character probabilities in an insert state (-insconf) match_jump_conf (Float) Confidence in the regularizer for transitions leaving a match state (-match_jump_conf) matchconf (Float) Confidence in the regularizer for character probabilities in a match state (-matchconf) mainline_cutoff (Float) Confidence in the regularizer for transitions leaving a match state (-mainline_cutoff) binary_output (Switch) Write models in binary format (-binary_output)

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/MailList.shtml - 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.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/modelfromalign.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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