Bio::Tools::Run::PiseApplication::bambe(3)

NAME
Bio::Tools::Run::PiseApplication::bambe

SYNOPSIS
  #

DESCRIPTION
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)

FEEDBACK

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

  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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR
Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT
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.

DISCLAIMER
This software is provided "as is" without warranty of any kind.

SEE ALSO

•   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.