Bio::Tools::Run::PiseApplication::bambe # Bio::Tools::Run::PiseApplication::bambe Bioperl class for: BAMBE Bayesian Analysis in Molecular Biology and Evolution (Simon, Larget) References: Larget, B. and D. Simon (1999). Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Molecular Biology and Evolution 16:750-759. Simon, D. and B. Larget. 1998. Bayesian analysis in molecular biology and evolution (BAMBE), version 1.01 beta. Department of Mathematics and Computer Science, Duquesne University. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/bambe.html for available values): bambe (String) data_file (Sequence) Alignment file (data-file) pipe: readseq_ok_alig bambe_format (Switch) Alignement file in BAMBE format ? seed (Integer) Seed for random number generator (seed) cycles (Integer) Number of cycles to run the main algorithm (cycles) main_algorithm (Excl) Algorithm to run during production cycles (main-algorithm) burn (Integer) Number of cycles to run the burn algorithm (burn) burn_algorithm (Excl) Algorithm to run during burn (burn-algorithm) use_beta (Switch) Use scaled beta distribution modification of the local algorithm (use-beta) molecular_clock (Switch) Use a molecular clock (molecular-clock) likelihood_model (Excl) Likelihood model (molecular-clock) category_list (String) A valid category list (category-list) single_kappa (Switch) Single kappa (single-kappa) initial_kappa (String) Comma separated list of positive kappa values (initial-kappa) initial_theta (String) Comma separated list of positive theta values (initial-theta) estimate_pi (Switch) Use empirical relative frequencies (estimate-pi) initial_pia (String) Comma separated list of initial stationary probability of base A (initial-pia) initial_pig (String) >Comma separated list of initial stationary probability of base G (initial-pig) initial_pic (String) >Comma separated list of initial stationary probability of base C (initial-pia) initial_pit (String) >Comma separated list of initial stationary probability of base T (initial-pia) initial_ttp (String) Comma separated list of positive transition/transversion parameter values (TN93 model) (initial-ttp) initial_gamma (String) Comma separated list of positive gamma values ((TN93 model) (initial-gamma) parameter_update_interval (Integer) Parameter update interval (parameter-update-interval) update_kappa (Switch) Update kappa value (update-kappa) update_theta (Switch) Update theta value (update-theta) update_pi (Switch) Update pi value (update-pi) update_ttp (Switch) Update tpp value (TN93 model) (update-ttp) update_gamma (Switch) Update gamma value for (TN93 model) (update-gamma) tune_interval (Integer) Tune interval (tune-interval) global_tune (Float) Half-window width for global (global-tune) local_tune (Float) Stretch parameter for local (local-tune) theta_tune (Float) Dirichlet parameter for theta update (theta-tune) pi_tune (Float) Dirichlet parameter for pi update (pi-tune) kappa_tune (Float) Halft window width for kappa update (kappa-tune) ttp_tune (Float) Halft window width for tpp update (TN93 model) (tpp-tune) gamma_tune (Float) Half window width for gamma update (TN93 model) (gamma-tune) beta_tune (Float) Beta parameter for local update (beta-tune) sample_interval (Integer) Sample interval (sample-interval) newick_format (Switch) Newick format of tree file (newick-format) file_root (String) outgroup (Integer) Outgroup tree_file (InFile) Tree file (tree-file) init_tree_type (Excl) Initial tree type (initial-tree-type) max_initial_tree_height (Float) Initial tree height used to generate an initial random tree (max-initial-tree-height)

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/bambe.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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