Bio::Tools::Run::PiseApplication::protdist # Bio::Tools::Run::PiseApplication::protdist Bioperl class for: Phylip protdist - Program to compute distance matrix from protein sequences (Felsenstein) References: Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle. Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/protdist.html for available values): protdist (String) infile (Sequence) Alignement File pipe: readseq_ok_alig method (Excl) Distance model (P) gamma_dist (Excl) Gamma distribution of rates among positions (G) seqboot (Switch) Perform a bootstrap before analysis resamp_method (Excl) Resampling methods seqboot_seed (Integer) Random number seed (must be odd) replicates (Integer) How many replicates weights (Switch) Use weights for sites (W) weights_file (InFile) Weights file multiple_dataset (String) bootconfirm (String) bootterminal_type (String) printdata (Switch) Print out the data at start of run (1) code (Excl) Genetic code (U) categorization (Excl) Categorization of amino acids (A) change_prob (Integer) Prob change category (1.0=easy) (E) ratio (Integer) Transition/transversion ratio (T) base_frequencies (Integer) Base frequencies for A, C, G, T/U (separated by commas) confirm (String) terminal_type (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/protdist.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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