Bio::Tools::Run::Phylo::PAML::Codeml(3pm)		User Contributed Perl Documentation		 Bio::Tools::Run::Phylo::PAML::Codeml(3pm)

NAME

       Bio::Tools::Run::Phylo::PAML::Codeml - Wrapper aroud the PAML program codeml

SYNOPSIS

	 use Bio::Tools::Run::Phylo::PAML::Codeml;
	 use Bio::AlignIO;

	 my $alignio = Bio::AlignIO->new(-format => 'phylip',
					-file	=> 't/data/gf-s85.phylip');

	 my $aln = $alignio->next_aln;

	 my $codeml = Bio::Tools::Run::Phylo::PAML::Codeml->new();
	 $codeml->alignment($aln);
	 my ($rc,$parser) = $codeml->run();
	 my $result = $parser->next_result;
	 my $MLmatrix = $result->get_MLmatrix();
	 print "Ka = ", $MLmatrix->[0]->[1]->{'dN'},"
";
	 print "Ks = ", $MLmatrix->[0]->[1]->{'dS'},"
";
	 print "Ka/Ks = ", $MLmatrix->[0]->[1]->{'omega'},"
";

DESCRIPTION

       This is a wrapper around the codeml 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 codeml.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/wiki/Mailing_lists	- 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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason-at-bioperl-dot-org

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 codeml programs are listed below.  The default values are always the first one listed.  These descriptions are
       essentially lifted from the example codeml.ctl file and pamlDOC documentation provided by the author.

       CodonFreq specifies the equilibrium codon frequencies in codon substitution model. These frequencies can be assumed to be equal (1/61 each
       for the standard genetic code, CodonFreq = 0), calculated from the average nucleotide frequencies (CodonFreq = 1), from the average
       nucleotide frequencies at the three codon positions (CodonFreq = 2), or used as free parameters (CodonFreq = 3). The number of parameters
       involved in those models of codon frequencies is 0, 3, 9, and 60 (under the universal code), for CodonFreq = 0, 1, 2, and 3 respectively.

       aaDist specifies whether equal amino acid distances are assumed (= 0) or Grantham's matrix is used (= 1) (Yang et al. 1998).

       runmode = -2 performs ML estimation of dS and dN in pairwise comparisons. The program will collect estimates of dS and dN into the files
       2ML.dS and 2ML.dN. Since many users seem interested in looking at dN /dS ratios among lineages, examination of the tree shapes indicated by
       branch lengths calculated from the two rates may be interesting although the analysis is ad hoc. If your species names have no more than 10
       characters, you can use the output distance matrices as input to Phylip programs such as neighbor without change. Otherwise you need to
       edit the files to cut the names short.

       model concerns assumptions about the dN/dS rate ratios among branches (Yang 1998; Yang and Nielsen 1998). model =0 means a single dN/dS
       ratio for all lineages (branches), 1 means one ratio for each branch (free ratio model), and 2 means arbitrary number of rations (such as
       the 2-ratios or 3-ratios models. with model =2, you may specify the omega ratios for the branches using branch labels (read about the tree
       structure file in the document).  This option seems rather easy to use. Otherwise, the program will ask the user to input a branch mark for
       the dN/dS ratio assumed for each branch. This should be an integral number between 0 to k - 1 if k different dN/dS ratios (omega_0 -
       omega_k - 1) are assumed for the branches of the tree. Bioperl note basically, doing this interactively is not going to work very well, so
       this module is really focused around using the 0 or 1 parameters.  Read the program documentation if you'd like some more detailed
       instructions.

       NSsites specifies models that allow the dN/dS ratio (omega) to vary among sites (Nielsen and Yang 1998, Yang et al. 2000) Nssites = m
       corresponds to model Mm in Yang et al(2000).  The variable ncatG is used to specify the number of categories in the omega distribution
       under some models.  The values of ncatG() used to perform our analyses are 3 for M3 (discrete), 5 for M4 (freq), 10 for the continuous
       distributions (M5: gamma, M6: 2gamma, M7: beta, M8:beta&w, M9:beta&gamma, M10: beta&gamma+1, M11:beta&normal>1, and
       M12:0&2normal>1, M13:3normal>0). This means M8 will have 11 site classes (10 from the beta distribution plus 1 additional class).
       The posterior probabilities for site classes as well as the expected omega values for sites are listed in the file rst, which may be useful
       to pinpoint sites under positive selection, if they exist.

       To make it easy to run several Nssites models in one go, the executable Bio::Tools::Run::Phylo::PAML::Codemlsites can be used, which asks
       you how many and which models to run at the start of the program. The number of categories used will then match those used in Yang et
       al(2000).

       As noted in that paper, some of the models are hard to use, in particular, M12 and M13. Recommended models are 0 (one-ratio), 1 (neutral),
       2 (selection), 3 (discrete), 7 (beta), and 8 (beta&omega ). Some of the models like M2 and M8 are noted to be prone to the problem of
       multiple local optima. You are advised to run the program at least twice, once with a starting omega value <1 and a second time with a
       value >1, and use the results corresponding to the highest likelihood. The continuous neutral and selection models of Nielsen and Yang(1998) are not implemented in the program.

       icode for genetic code and these correspond to 1-11 in the genbank transl table.
	 0:universal code
	 1:mamalian mt
	 2:yeast mt
	 3:mold mt,
	 4:invertebrate mt
	 5:ciliate nuclear
	 6:echinoderm mt
	 7:euplotid mt
	 8:alternative yeast nu.
	 9:ascidian mt
	 10:blepharisma nu

       RateAncestor For codon sequences, ancestral reconstruction is not implemented for the models of variable dN/dS ratios among sites. The
       output under codon-based models usually shows the encoded amino acid for each codon. The output under "Prob of best character at each node,
       listed by site" has two posterior probabilities for each node at each codon (amino acid) site. The first is for the best codon. The second,
       in parentheses, is for the most likely amino acid under the codon substitution model. This is a sum of posterior probabilities across
       synonymous codons. In theory it is possible although rare for the most likely amino acid not to match the most likely codon.

       Output for codon sequences (seqtype = 1): The codon frequencies in each sequence are counted and listed in a genetic code table, together
       with their sums across species. Each table contains six or fewer species. For data of multiple genes (option G in the sequence file), codon
       frequencies in each gene (summed over species) are also listed. The nucleotide distributions at the three codon positions are also listed.
       The method of Nei and Gojobori(1986) is used to calculate the number of synonymous substitutions per synonymous site (dS ) and the number
       of nonsynonymous substitutions per nonsynonymous site (dN ) and their ratio (dN /dS ). These are used to construct initial estimates of
       branch lengths for the likelihood analysis but are not MLEs themselves. Note that the estimates of these quantities for the a- and b-globin
       genes shown in Table 2 of Goldman and Yang(1994), calculated using the MEGA package (Kumar et al., 1993), are not accurate.

       Results of ancestral reconstructions (RateAncestor = 1) are collected in the file rst. Under models of variable dN/dS ratios among sites
       (NSsites models), the posterior probabilities for site classes as well as positively selected sites are listed in rst.

       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::Codeml->new();
	Function: Builds a new Bio::Tools::Run::Phylo::PAML::Codeml object
	Returns : Bio::Tools::Run::Phylo::PAML::Codeml
	Args	: -alignment => the Bio::Align::AlignI object
		  -save_tempfiles => boolean to save the generated tempfiles and
				     NOT cleanup after onesself (default FALSE)
		  -tree => the Bio::Tree::TreeI object
		  -branchlengths => 0: ignore any branch lengths found on the tree
				    1: use as initial values
				    2: fix branch lengths
		  -params => a hashref of PAML parameters (all passed to set_parameter)
		  -executable => where the codeml executable resides

       See also: Bio::Tree::TreeI, Bio::Align::AlignI

   prepare
	Title	: prepare
	Usage	: my $rundir = $codeml->prepare($aln);
	Function: prepare the codeml 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) = $codeml->run($aln,$tree);
	Function: run the codeml 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 analysus run is stored.
	Returns : value of error_string
	Args	: newvalue (optional)

   alignment
	Title	: alignment
	Usage	: $codeml->align($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	: $codeml->tree($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	: $codeml->set_parameter($param,$val);
	Function: Sets a codeml 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:
		    $codeml->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	: $codeml->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)

   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 = $codeml->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	: $codeml->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

perl v5.12.3							    2011-06-18				 Bio::Tools::Run::Phylo::PAML::Codeml(3pm)