Provided by: libbio-perl-run-perl_1.6.9-2_all 
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'},"\n";
print "Ks = ", $MLmatrix->[0]->[1]->{'dS'},"\n";
print "Ka/Ks = ", $MLmatrix->[0]->[1]->{'omega'},"\n";
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