Bio::Tools::Run::PiseApplication::lvb # Bio::Tools::Run::PiseApplication::lvb Bioperl class for: LVB Reconstructing Evolution With Parsimony And Simulated Annealing (D. Barker) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/lvb.html for available values): lvb (String) infile (Sequence) Alignement File pipe: readseq_ok_alig convert (Switch) Convert the alignment file to LVB format method (Excl) Search method (method) seed (Integer) Seed for the random number generator (seed) t0 (Float) Initial temperature (0 < t0 <= 1.0) (t0) t1 (Float) Second temperature (0 < t1 <= 1.0 and t1 < t0) (t1) maxaccept (Integer) How many new trees are accepted (maxaccept) maxpropose (Integer) How many changes are proposed (maxpropose) maxfail (Integer) How many 'failed' successive temperatures to allow (maxfail) equivalent (Excl) Equivalent characters sets (equivalent) matchchar (Switch) Mark similar characters relative to the first row by a dot (matchchar) ignorechars (Excl) Ignore characters containing (ignorechars) outgroup (String) Name of the outgroup (outgroup) runs (Integer) Number of runs (runs) verbose (Switch) Statistics (verbose) titleprec (Switch) Comment out titles in tabulated statistics (titleprec)

Mailing Lists
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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/lvb.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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