Provided by: libbio-tools-phylo-paml-perl_1.7.3-2_all bug


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


       version 1.7.3


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


       This is a wrapper around the codeml program of PAML (Phylogenetic Analysis by Maximum
       Likelihood) package of Ziheng Yang.  See
       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.

   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

       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.



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

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

        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)

        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>

        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

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

        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)

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

        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

        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


        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

        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]

        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]

        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

        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:
        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()>

        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

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

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

Bio::Tools::Run::WrapperBase methods


   Mailing lists
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       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.
              - General discussion    - About the mailing lists

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

       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:


       Jason Stajich <>


       This software is copyright (c) by Jason Stajich <>.

       This software is available under the same terms as the perl 5 programming language system