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/

Default Values¶

INCOMPLETE DOCUMENTATION OF ALL METHODS

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
format

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
data.
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
similarities.
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
constants).
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

Site
Number of sites in alignment

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

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

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

LRT_Stat
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)

Pval
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).

Result
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

Note

  The following events are flagged:
  Synonymous            All codons at a site code for the same amino 
                        acid.
  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
                        character.
  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.

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::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

prepare¶

 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

run¶

 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

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   : $slr->align($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>

tree¶

 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>

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   : $slr->set_parameter($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:
             $slr->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   : $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

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 = $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

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