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Bio-Tools-Phylo-PAML-1.7.3
River stage one • 1 direct dependent • 1 total dependent
/ Bio::Tools::Run::Phylo::PAML::Baseml

NAME

Bio::Tools::Run::Phylo::PAML::Baseml - Wrapper aroud the PAML program baseml

VERSION

version 1.7.3

SYNOPSIS

use Bio::Tools::Run::Phylo::PAML::Baseml;
use Bio::AlignIO;
my $alignio = Bio::AlignIO->new(-format => 'phylip',
                      -file   => 't/data/gf-s85.phylip');
my $aln = $alignio->next_aln;

my $bml = Bio::Tools::Run::Phylo::PAML::Baseml->new();
$bml->alignment($aln);
my ($rc,$parser) = $bml->run();
while( my $result = $parser->next_result ) {
  my @otus = $result->get_seqs();
  my $MLmatrix = $result->get_MLmatrix();
  # 0 and 1 correspond to the 1st and 2nd entry in the @otus array
}

DESCRIPTION

This is a wrapper around the baseml 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 will generate a proper baseml.ctl file and will run the program in a separate temporary directory to avoid creating temp files all over the place and will cleanup after itself..

The values you can feed to the configuration file are documented here.

'noisy'   => [ 0..3,9],
'verbose' => [ 0,1,2], # 0:concise, 1:detailed, 2:too much
'runmode' => [0..5],
# for runmode
# 0: use the provided tree structure(s) in treefile
# 1,2: mean heuristic search by star-decomposition alg
# 2: starts from star tree while 1 reads a multifurcating
# tree from treefile and ties to estimate the best
# bifurcating tree
# 3: stepwise addition
# 4: NNI perturbation with the starting tree
# Tree search DOES NOT WORK WELL so estimate a tree
# using other programs first
'model'   => '0',
# for model
# 0: JC69 (uncorrected)
# 1: K80  (transitions/transversion weighted differently)
# 2: F81
# 3: F84
# 4: HKY85
# 5: T92 (Tamura 92)
# 6: TN93 (Tajima-Nei) correct for multiple substitutions
# 7: REV (aka GTR)
# 8: UNREST
# 9: REVu
#10: UNRESTu
# See Yang 1994 JME 39:105-111

# model 8 special case of the REV model
# model 9 is special case of unrestricted model
# can also supply special rate parameters
# so for example (from pamlDOC.pdf
# $model  = '8 [2 (CT) (AG)]'; # TN93
# $model  = '8 [2 (TA AT TG CA CG) (AG)]'; # TN93
# $model  = '9 [1 (TC CT AG GA)]; # K80
# $model  = '9 [0]'; # JC69
# $model  = '9 [11 (TA) (TG) (CT) (CA) (CG) (AT) (AC) (AG) (GT) (GC) (GA)],

'outfile' => 'mlb',
'fix_kappa'=> [0,1], # 0:estimate kappa, 1:fix kappa
'kappa'    => '2.5', # initial or fixed kappa
'fix_alpha'=> [1,0], # 0: estimate gamma shape param
# 1: fix it at alpha
'alpha'    => '0', # initial of fixed alpha
# 0: infinity (constant rate)
'Malpha'   => [0,1], # different alphas for genes

'fix_rho'=> [1,0], # 0: estimate gamma shape param
                              # 1: fix it at alpha
'rho'    => '0', # initial of fixed alpha
# 0: infinity (constant rate)

'ncatG'    => '5', # number of categories in the dD,AdG, or nparkK models of rates
'nparK'    => [0..4], # rate-class models
# 1:rk 2:rk&fK
# 3:rK&MK(1/K) 4:rK&MK
'nhomo'    => [0..4], # 0 & 1: homogeneous,
# 2: kappa for brances
# 3:N1 4:N2
'getSE'    => [0,1],
'RateAncestor' => [1,0,2], # rates (alpha > 0) or
# ancestral states
'cleandata' => [1,0], # remove sites with
# ambiguity data (1:yes or 0:no)

'fix_blength' => [-1,0,1,2], # 0: ignore, -1: random,
# 1: initial, 2: fixed

# 'icode'    => [ 0..10], # (with RateAncestor=1.
#try "GC" in data,model=4,Mgene=4)
'ndata'    => [5,1..10],
'clock'    => [0..3], # 0: no clock, 1: clock, 2: local clock, 3: CombinedAnalysis
'Small_Diff' => '1e-6', #underflow issues?

ATTRIBUTES

program_name

Title   : program_name
Usage   : $obj->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    :

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   : $baseml->alignment($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

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 = $baseml->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

METHODS

new

Title   : new
Usage   : my $obj = Bio::Tools::Run::Phylo::PAML::Baseml->new();
Function: Builds a new Bio::Tools::Run::Phylo::PAML::Baseml object
Returns : Bio::Tools::Run::Phylo::PAML::Baseml
Args    : -alignment => the L<Bio::Align::AlignI> object
          -tree => the L<Bio::Tree::TreeI> object if you want to use runmode
                   0 or 1
          -save_tempfiles => boolean to save the generated tempfiles and
                             NOT cleanup after onesself (default FALSE)

run

Title   : run
Usage   : $yn->run();
Function: run the Baseml analysis using the default or updated parameters
          the alignment parameter must have been set
Returns : 3 values,
          $rc = 1 for success, 0 for errors
          hash reference of the Yang calculated Ka/Ks values
                   this is a set of pairwise observations keyed as
                   sequencenameA->sequencenameB->datatype
          hash reference same as the previous one except it for the
          Nei and Gojobori calculated Ka,Ks,omega values
Args    : optionally, a value appropriate for alignment() and one for tree()
NB      : Since Baseml doesn't handle spaces in tree node ids, if a tree is
          in use spaces will be converted to underscores in both the tree node
          ids and alignment sequence ids.

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   : $baseml->set_parameter($param,$val);
Function: Sets a baseml parameter, will be validated against
          the valid values as set in the %VALIDVALUES class variable.
          The checks can be ignored if on turns of param checks like this:
            $baseml->no_param_checks(1)
Returns : boolean if set was success, if verbose is set to -1
          then no warning will be reported
Args    : $paramname => 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   : $baseml->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
NB      : using this isn't an especially good idea! You don't need to do
          anything to end up using default parameters: hence 'default'!

cleanup

Title   : cleanup
Usage   : $baseml->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

Bio::Tools::Run::Wrapper methods

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/Support.html    - 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:

https://github.com/bioperl/bio-tools-phylo-paml/issues

AUTHORS

Jason Stajich <jason@bioperl.org>

Sendu Bala <bix@sendu.me.uk>

COPYRIGHT

This software is copyright (c) by Jason Stajich <jason@bioperl.org>.

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