Bio::Tools::Run::PiseApplication::pars # Bio::Tools::Run::PiseApplication::pars Bioperl class for: Phylip pars - Discrete character parsimony (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/pars.html for available values): pars (String) infile (InFile) Input File search_opt (Excl) Search option (S) save_trees (Integer) Number of trees to save? (V) use_ancestral_state (Switch) Use ancestral states in input file (A) jumble (Switch) Randomize (jumble) input order (J) jumble_seed (Integer) Random number seed (must be odd) times (Integer) Number of times to jumble weights (Switch) Weighted sites (W) weight_file (InFile) Weight file user_tree (Switch) Use User tree (default: no, search for best tree) (U) tree_file (InFile) User Tree file tree_nb (Integer) How many tree(s) in the User Tree file multiple_dataset (Switch) Analyze multiple data sets (M) datasets_nb (Integer) How many data sets consense (Switch) Compute a consensus tree print_tree (Switch) Print out tree (3) print_step (Switch) Print out steps in each character (4) print_states (Switch) Print states 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) indent_tree (Switch) Indent treefile use_threshold (Switch) Use Threshold parsimony (T) threshold (Integer) Threshold value (if use threshold parsimony) outgroup (Integer) Outgroup root (default, use as outgroup species 1) (O) confirm (String) terminal_type (String) consense_confirm (String) consense_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/pars.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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