Bio::Tools::Run::Phylo::PAML::Evolver man page on Fedora

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Bio::Tools::Run::PhyloUserMContributedBio::Tools::Run::Phylo::PAML::Evolver(3)

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

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:

       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)

perl v5.14.1			  2011Bio::Tools::Run::Phylo::PAML::Evolver(3)
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