Provided by: libbio-perl-run-perl_1.7.1-3_all bug


       Bio::Tools::Run::Phylo::SLR - Wrapper around the SLR program


         use Bio::Tools::Run::Phylo::SLR;
         use Bio::AlignIO;
         use Bio::TreeIO;
         use Bio::SimpleAlign;

         my $alignio = Bio::AlignIO->new
             (-format => 'fasta',
              -file   => 't/data/219877.cdna.fasta');

         my $aln = $alignio->next_aln;

         my $treeio = Bio::TreeIO->new
             (-format => 'newick', -file => 't/data/219877.tree');

         my $tree = $treeio->next_tree;

         my $slr = Bio::Tools::Run::Phylo::SLR->new();
         # $rc = 1 for success, 0 for errors
         my ($rc,$results) = $slr->run();

         my $positive_sites = $results->{'positive'};

         print "# Site\tNeutral\tOptimal\tOmega\t",
         foreach my $positive_site (@$positive_sites) {
                 $positive_site->[0], "\t",
                 $positive_site->[1], "\t",
                 $positive_site->[2], "\t",
                 $positive_site->[3], "\t",
                 $positive_site->[4], "\t",
                 $positive_site->[5], "\t",
                 $positive_site->[6], "\t",
                 $positive_site->[7], "\t",
                 $positive_site->[8], "\t",


       This is a wrapper around the SLR program. See for more

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


   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.
                  - 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:

AUTHOR - Albert Vilella

       Email avilella-at-gmail-dot-com


       Additional contributors names and emails here


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

   Default Values

       seqfile [incodon]
         File from which to read alignment of codon sequences. The file
         should be in PAML format.

       treefile [intree]
         File from which tree should be read. The tree should be in Nexus

       outfile [slr.res]
         File to which results are written. If the file already exists, it will
         be overwritten.

       reoptimise [1]
         Should the branch lengths, omega and kappa be reoptimized?
         0 - no
         1 - yes.

       kappa [2.0]
         Value for kappa. If 'reoptimise' is specified, the value
         given will be used as am initial estimate,

       omega [0.1]
         Value for omega (dN/dS). If 'reoptimise' is specified, the value
         given will be used as an initial estimate.

       codonf [0]
         How codon frequencies are estimated:
           0: F61/F60  Estimates used are the empirical frequencies from the
           1: F3x4     The frequencies of nucleotides at each codon position
         are estimated from the data and then multiplied together to get the
         frequency of observing a given codon. The frequency of stop codons is
         set to zero, and all other frequencies scaled appropriately.
           2: F1x4     Nucleotide frequencies are estimated from the data
         (not taking into account at which position in the codon it occurs).
         The nucleotide frequencies are multiplied together to get the frequency
         of observing and then corrected for stop codons.

       freqtype [0]
         How codon frequencies are incorporated into the substitution matrix.
         0: q_{ij} = pi_{j} s_{ij}
         1: q_{ij} = \sqrt(pi_j/pi_i) s_{ij}
         2: q_{ij} = \pi_{n} s_{ij}, where n is the nucleotide that the
         subsitution is to.
         3: q_{ij} = s_{ij} / pi_i
         Option 0 is the tradition method of incorporating equilibrium frequencies
         into subsitution matrices (Felsenstein 1981; Goldman and Yang, 1994)
         Option 1 is described by Goldman and Whelan (2002), in this case with the
         additional parameter set to 0.5.
         Option 2 was suggested by Muse and Gaut (1994).
         Option 3 is included as an experiment, originally suggested by Bret Larget.
         it does not appear to describe evolution very successfully and should not
         be used for analyses.

         Kosakovsky-Pond has repeatedly stated that he finds incorporating codon
         frequencies in the manner of option 2 to be superior to option 0. We find
         that option 1 tends to perform better than either of these options.

       positive_only [0]
         If only positively selected sites are of interest, set this to "1".
         Calculation will be slightly faster, but information about sites under
         purifying selection is lost.

       gencode [universal]
         Which genetic code to use when determining whether a given mutation
         is synonymous or nonsynonymous. Currently only "universal" and
         "mammalian" mitochondrial are supported.

       nucleof [0]
         Allow for empirical exchangabilities for nucleotide substitution.
         0: No adjustment. All nucleotides treated the same, modulo
         transition / transversion.
         1: The rate at which a substitution caused a mutation from nucleotide
         a to nucleotide b is adjust by a constant N_{ab}. This adjustment is
         in addition to other adjustments (e.g. transition / transversion or
         base frequencies).

       aminof [0]
         Incorporate amino acid similarity parameters into substitution matrix,
         adjusting omega for a change between amino acid i and amino acid j.
         A_{ij} is a symmetric matrix of constants representing amino acid
         0: Constant omega for all amino acid changes
         1: omega_{ij} = omega^{A_{ij}}
         2: omega_{ij} = a_{ij} log(omega) / [ 1 - exp(-a_{ij} log(omega)) ]
         Option 1 has the same form as the original codon subsitution model
         proposed by Goldman and Yang (but with potentially different
         Option 2 has a more population genetic derivtion, with omega being
         interpreted as the ratio of fixation probabilities.

       nucfile [nuc.dat]
         If nucleof is non-zero, read nucleotide substitution constants from
         nucfile. If this file does not exist, hard coded constants are used.

       aminofile [amino.dat]
         If aminof is non-zero, read amino acid similarity constants from
         aminofile. If this file does not exist, hard coded constants are used.

       timemem [0]
         Print summary of real time and CPU time used. Will eventually print
         summary of memory use as well.

       ldiff [3.841459]
         Twice log-likelihood difference used as a threshold for calculating
         support (confidence) intervals for sitewise omega estimates. This
         value should be the quantile from a chi-square distribution with one
         degree of freedom corresponding to the support required.
         E.g. qchisq(0.95,1) = 3.841459
            0.4549364 = 50% support
            1.323304  = 75% support
            2.705543  = 90% support
            3.841459  = 95% support
            6.634897  = 99% support
            7.879439  = 99.5% support
           10.82757   = 99.9% support

       paramin []
         If not blank, read in parameters from file given by the argument.

       paramout []
         If not blank, write out parameter estimates to file given.

       skipsitewise [0]
         Skip sitewise estimation of omega. Depending on other options given,
         either calculate maximum likelihood or likelihood fixed at parameter
         values given.

       seed [0]
         Seed for random number generator. If seed is 0, then previously
         produced seed file (~/.rng64) is used. If this does not exist, the
         random number generator is initialised using the clock.

       saveseed [1]
         If non-zero, save finial seed in file (~/.rng64) to be used as initial
         seed in future runs of program.

   Results Format
       Results file (default: slr.res) ------------ Results are presented in nine columns

         Number of sites in alignment

         (minus) Log-probability of observing site given that it was
         evolving neutrally (omega=1)

         (minus) Log-probability of observing site given that it was
         evolving at the optimal value of omega.

         The value of omega which maximizes the log-probability of observing

         Log-likelihood ratio statistic for non-neutral selection (or
         positive selection if the positive_only option is set to 1).
         LRT_Stat = 2 * (Neutral-Optimal)

         P-value for non-neutral (or positive) selection at a site,
         unadjusted for multiple comparisons.

       Adj. Pval
         P-value for non-neutral (or positive) selection at a site, after
         adjusting for multiple comparisons using the Hochberg procedure
         (see the file "MultipleComparisons.txt" in the doc directory).

         A simple visual guide to the result. Sites detected as having been
         under positive selection are marked with a '+', sites under
         purifying selection are marked with '-'. The number of symbols
           Number symbols      Threshold
                 1             95%
                 2             99%
                 3             95% after adjustment
                 4             99% after adjustment

         Occasionally the result may also contain an exclamation mark. This
         indicates that the observation at a site is not significantly
         different from random (equivalent to infinitely strong positive
         selection). This may indicate that the alignment at that site is bad


         The following events are flagged:
         Synonymous            All codons at a site code for the same amino
         Single character      Only one sequence at the site is ungapped,
                               the result of a recent insertion for example.
         All gaps              All sequences at a site contain a gap

         Sites marked "Single character" or "All gaps" are not counted
         towards the number of sites for the purposes of correcting for
         multiple comparisons since it is not possible to detect selection
         from none or one observation under the assumptions made by the
         sitewise likelihood ratio test.

        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   : new
        Usage   : my $obj = Bio::Tools::Run::Phylo::SLR->new();
        Function: Builds a new Bio::Tools::Run::Phylo::SLR object
        Returns : Bio::Tools::Run::Phylo::SLR
        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
                  -params => a hashref of SLR parameters (all passed to set_parameter)
                  -executable => where the SLR executable resides

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

        Title   : prepare
        Usage   : my $rundir = $slr->prepare($aln);
        Function: prepare the SLR 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

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

        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   : $slr->align($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   : $slr->tree($tree, %params);
        Function: Get/Set the L<Bio::Tree::TreeI> object
        Returns : L<Bio::Tree::TreeI>
        Args    : [optional] $tree => L<Bio::Tree::TreeI>,

        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   : 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   : $slr->set_parameter($param,$val);
        Function: Sets a SLR 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   : $slr->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

        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 = $slr->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   : cleanup
        Usage   : $slr->cleanup();
        Function: Will cleanup the tempdir directory after an SLR 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