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.

  [email protected]              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

Support

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

[email protected]

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:

option1 specifies something.

option2 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)