Bio::Tools::Run::PiseApplication::protpars # Bio::Tools::Run::PiseApplication::protpars Bioperl class for: Phylip protpars - Protein Sequence Parcimony Method (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/protpars.html for available values): protpars (String) infile (Sequence) Alignement File pipe: readseq_ok_alig use_threshold (Switch) Use Threshold parsimony (T) threshold (Integer) Threshold value (if use threshold parsimony) code (Excl) Genetic code (U) jumble (Switch) Randomize (jumble) input order of sequences (J) jumble_seed (Integer) Jumble random number seed (must be odd) times (Integer) Number of times to jumble seqboot (Switch) Perform a bootstrap before analysis method (Excl) Resampling methods seqboot_seed (Integer) Random number seed (must be odd) replicates (Integer) How many replicates consense (Switch) Compute a consensus tree user_tree (Switch) Use User tree (default: no, search for best tree) (U) tree_file (InFile) User Tree file print_tree (Switch) Print out tree (3) print_sequences (Switch) Print sequences at all nodes of tree (5) print_treefile (Switch) Write out trees onto tree file (6) printdata (Switch) Print out the data at start of run (1) print_steps (Switch) Print out steps in each site (4) indent_tree (Switch) Indent treefile outgroup (Integer) Outgroup species (default, use as outgroup species 1) (O) confirm (String) terminal_type (String) multiple_dataset (String) bootconfirm (String) bootterminal_type (String) consense_confirm (String) consense_terminal_type (String) consense_outgroup (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/protpars.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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