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Manual Reference Pages  -  BIO::TOOLS::RUN::PHYLO::PAML::EVOLVER (3)

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NAME

Bio::Tools::Run::Phylo::PAML::Evolver - Wrapper aroud the PAML program evolver

CONTENTS

SYNOPSIS



  use Bio::Tools::Run::Phylo::PAML::Evolver;

  my $evolver = Bio::Tools::Run::Phylo::PAML::Evolver->new();

  # Get a $tree object somehow
  $evolver->tree($tree);

  # FIXME: evolver generates a tree (first run with option 1 or 2)?

  # One or more alns are created
  my @alns = $evolver->run();

  ####

  # Or with all the data coming from a previous PAML run
  my $parser = Bio::Tools::Phylo::PAML->new
    (
     -file => "$inputfile",
    );
  my $result = $parser->next_result();
  my $tree = $result->next_tree;
  $evolver->tree($tree);
  my @codon_freqs = $result->get_CodonFreqs();
  $evolver->set_CodonFreqs(\@codon_freqs);

  my $val = $evolver->prepare();

  # FIXME: something similar for nucleotide frequencies:
  # Option (5) Simulate nucleotide data sets (use MCbase.dat)?

  # FIXME: something similar for aa parameters:
  # Option (7) Simulate amino acid data sets (use MCaa.dat)?

  # FIXME: With an initial RootSeq.txt



DESCRIPTION

This is a wrapper around the evolver program of PAML (Phylogenetic Analysis by Maximum Likelihood) package of Ziheng Yang. See http://abacus.gene.ucl.ac.uk/software/paml.html for more information.

This module is more about generating the properl MCmodel.ctl file and will run the program in a separate temporary directory to avoid creating temp files all over the place.

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



    Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

    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://bioperl.org/bioperl-bugs/



AUTHOR - Albert Vilella

Email avilella-AT-gmail-DOT-com

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

    Default Values

Valid and default values for evolver programs are listed below. The default values are always the first one listed. These descriptions are essentially lifted from the example MCcodon.dat file and pamlDOC documentation provided by the author.

Stub:

<B>option1B> specifies something.

<B>option2B> specifies something else.

INCOMPLETE DOCUMENTATION OF ALL METHODS

    program_name



 Title   : program_name
 Usage   : $factory->program_name()
 Function: holds the program name
 Returns:  string
 Args    : None



    program_dir



 Title   : program_dir
 Usage   : ->program_dir()
 Function: returns the program directory, obtained from ENV variable.
 Returns:  string
 Args    :



    new



 Title   : new
 Usage   : my $obj = Bio::Tools::Run::Phylo::PAML::Evolver->new();
 Function: Builds a new Bio::Tools::Run::Phylo::PAML::Evolver object
 Returns : Bio::Tools::Run::Phylo::PAML::Evolver
           -save_tempfiles => boolean to save the generated tempfiles and
                              NOT cleanup after onesself (default FALSE)
           -tree => the Bio::Tree::TreeI object (FIXME: optional if this is done in a first run)
           -params => a hashref of PAML parameters (all passed to set_parameter)
           -executable => where the evolver executable resides



See also: Bio::Tree::TreeI

    prepare



 Title   : prepare
 Usage   : my $rundir = $evolver->prepare($aln);
 Function: prepare the evolver analysis using the default or updated parameters
           the alignment parameter must have been set
 Returns : value of rundir
 Args    : L<Bio::Align::AlignI> object,
           L<Bio::Tree::TreeI> object [optional]



    run



 Title   : run
 Usage   : my ($rc,$parser) = $evolver->run();
 Function: run the evolver analysis using the default or updated parameters
           the alignment parameter must have been set
 Returns : Return code, L<Bio::Tools::Phylo::PAML>
 Args    : L<Bio::Align::AlignI> object,
           L<Bio::Tree::TreeI> object [optional]



    error_string



 Title   : error_string
 Usage   : $obj->error_string($newval)
 Function: Where the output from the last analysis run is stored.
 Returns : value of error_string
 Args    : newvalue (optional)



    alignment



 Title   : alignment
 Usage   : $evolver->align($aln);
 Function: Get/Set the L<Bio::Align::AlignI> object
 Returns : L<Bio::Align::AlignI> object
 Args    : [optional] L<Bio::Align::AlignI>
 Comment : We could potentially add support for running directly on a file
           but we shall keep it simple
 See also: L<Bio::SimpleAlign>



    tree



 Title   : tree
 Usage   : $evolver->tree($tree, %params);
 Function: Get/Set the L<Bio::Tree::TreeI> object
 Returns : L<Bio::Tree::TreeI>
 Args    : [optional] $tree => L<Bio::Tree::TreeI>,
           [optional] %parameters => hash of tree-specific parameters:
                  branchLengths: 0, 1 or 2
                  out

 Comment : We could potentially add support for running directly on a file
           but we shall keep it simple
 See also: L<Bio::Tree::Tree>



    get_parameters



 Title   : get_parameters
 Usage   : my %params = $self->get_parameters();
 Function: returns the list of parameters as a hash
 Returns : associative array keyed on parameter names
 Args    : none



    set_parameter



 Title   : set_parameter
 Usage   : $evolver->set_parameter($param,$val);
 Function: Sets a evolver parameter, will be validated against
           the valid values as set in the %VALIDVALUES class variable. 
           The checks can be ignored if one turns off param checks like this:
             $evolver->no_param_checks(1)
 Returns : boolean if set was success, if verbose is set to -1
           then no warning will be reported
 Args    : $param => name of the parameter
           $value => value to set the parameter to
 See also: L<no_param_checks()>



    set_default_parameters



 Title   : set_default_parameters
 Usage   : $evolver->set_default_parameters(0);
 Function: (Re)set the default parameters from the defaults
           (the first value in each array in the
            %VALIDVALUES class variable)
 Returns : none
 Args    : boolean: keep existing parameter values



Bio::Tools::Run::WrapperBase methods

    no_param_checks



 Title   : no_param_checks
 Usage   : $obj->no_param_checks($newval)
 Function: Boolean flag as to whether or not we should
           trust the sanity checks for parameter values 
 Returns : value of no_param_checks
 Args    : newvalue (optional)



    set_CodonFreqs



 Title   : set_CodonFreqs
 Usage   : $obj->set_CodonFreqs($newval)
 Function: Get/Set the Codon Frequence table
 Returns : value of set_CodonFreqs (a scalar)
 Args    : on set, new value (a scalar or undef, optional)



    get_CodonFreqs



 Title   : get_CodonFreqs
 Usage   : my @codon_freqs = $evolver->get_CodonFreqs()
 Function: Get the Codon freqs
 Returns : Array
 Args    : none



    save_tempfiles



 Title   : save_tempfiles
 Usage   : $obj->save_tempfiles($newval)
 Function:
 Returns : value of save_tempfiles
 Args    : newvalue (optional)



    outfile_name



 Title   : outfile_name
 Usage   : my $outfile = $evolver->outfile_name();
 Function: Get/Set the name of the output file for this run
           (if you wanted to do something special)
 Returns : string
 Args    : [optional] string to set value to



    tempdir



 Title   : tempdir
 Usage   : my $tmpdir = $self->tempdir();
 Function: Retrieve a temporary directory name (which is created)
 Returns : string which is the name of the temporary directory
 Args    : none



    cleanup



 Title   : cleanup
 Usage   : $evolver->cleanup();
 Function: Will cleanup the tempdir directory after a PAML run
 Returns : none
 Args    : none



    io



 Title   : io
 Usage   : $obj->io($newval)
 Function:  Gets a L<Bio::Root::IO> object
 Returns : L<Bio::Root::IO>
 Args    : none



    indel



 Title   : indel
 Usage   : $obj->indel($newval)
 Function: this is only useful if using evolver_indel instead of main
           evolver package:
           Exploring the Relationship between Sequence Similarity and
           Accurate Phylogenetic Trees Brandi L. Cantarel, Hilary
           G. Morrison and William Pearson
 Example :
 Returns : value of indel (a scalar)
 Args    : on set, new value (a scalar or undef, optional)



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perl v5.20.3 BIO::TOOLS::RUN::PHYLO::PAML::EVOLVER (3) 2016-04-05

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