NAME

Bio::Tools::Run::PiseApplication::tipdate

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::tipdate

      Bioperl class for:

        TipDate Analysis of trees with dated tips (Andrew Rambaut)

        References:

                Andrew Rambaut, 2000. Estimating the rate of molecular evolution: Incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics.



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/tipdate.html 
         for available values):


                tipdate (String)

                alignment (Sequence)
                        Alignment file
                        pipe: readseq_ok_alig

                model (Excl)
                        MODEL (-m)

                constant_rate (Switch)
                        Molecular clock model (SR model) (-k)

                change_rate (Excl)
                        Estimate rate of change of rate (VRDT model: requires dated tips)

                change_rate_value (Integer)
                        You may provide a constant rate value (-w #)

                absolute_rate (Float)
                        Estimate absolute rate of substitution (SRDT model: requires dated tips) (+s)Absolute rate of molecular evolution (requires dated tips) (-s)

                absolute_rate_value (Integer)
                        specify absolute rate of substitution (-s #)

                likelihood_root (Switch)
                        Estimate maximum likelihood root (requires molecular clock)

                absolute_root_value (Integer)
                        root with specified outgroup taxa (requires molecular clock) (-r #)

                absolute_rate (Float)
                        Estimate absolute rate of substitution (SRDT model: requires dated tips) (+s)Absolute rate of molecular evolution (requires dated tips) (-s)

                estimate_root (Switch)
                        Estimate maximum likelihood root (requires molecular clock) (+r)

                outgroup (Integer)
                        Root with specified outgroup taxa (requires molecular clock) (-r)

                substitution_confidence (Switch)
                        Estimate confidence intervals for rate of substitution (with +s option) (-is)

                date_confidence (Switch)
                        Estimate confidence intervals for date of root of tree (with +s option) (-id)

                change_confidence (Switch)
                        Estimate confidence intervals for rate of change of rate of substitution (with +w option) (-iw)

                limit (Float)
                        Limit to use estimating confidence intervals (-l)

                codon_categories (String)
                        CODON CATEGORIES = 112, 123, 120, etc. [default: homogeneity] (-p)

                codon_rate (String)
                        CODON category rates: #1 #2 #3 separated by commas [default = estimate rates] (-c)

                seperate (Switch)
                        Estimate seperate models for each site category (-e)

                gamma (Integer)
                        Num categories for gamma rate heterogeneity (2 to 32) (-g)

                alpha (Integer)
                        gamma shape (alpha) for site rate heterogeneity (-a)

                datasets (Integer)
                        Number of Datasets (-n)

                user_branch (Switch)
                        User branch-lengths [default = estimate] (-ul)

                treefile (InFile)
                        Optional file containing trees

                equal_freq (Switch)
                        Frequences of bases equal (-f=)

                freq_bases (String)
                        Frequences of bases: #A #C #G #T separated by commas(-f)

                transition_transversion (Float)
                        Transition/transversion ratio (-t)

                branch (Switch)
                        Print final branch lengths (-vb)

                likelihoods (Switch)
                        Write likelihoods for each Site (-vs)

                notrees (Switch)
                        Don't Write trees (-vw)

                memory (Switch)
                        Memory usage information (-vm)

                progress (Switch)

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/wiki/Mailing_lists  - 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 the web:

  http://bugzilla.open-bio.org/

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/tipdate.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

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