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Bio::Phylo::Models::SuUsertContributedBPo::Phylo::Models::Substitution::Dna(3)

NAME
       Bio::Phylo::Models::Substitution::Dna - DNA substitution	model

SYNOPSIS
	   use Bio::Phylo::Models::Substitution::Dna;

	   # create a DNA substitution model from scratch
	   my $model = Bio::Phylo::Models::Substitution::Dna->new(
	       '-type'	 => 'GTR',
	       '-pi'	 => [ 0.23, 0.27, 0.24,	0.26 ],
	       '-kappa'	 => 2,
	       '-alpha'	 => 0.9,
	       '-pinvar' => 0.5,
	       '-ncat'	 => 6,
	       '-median' => 1,
	       '-rate'	 => [
		   [ 0.23, 0.23, 0.23, 0.23 ],
		   [ 0.23, 0.26, 0.26, 0.26 ],
		   [ 0.27, 0.26, 0.26, 0.26 ],
		   [ 0.24, 0.26, 0.26, 0.26 ]
	       ]
	   );

	   # get substitution rate from	A to C
	   my $rate = $model->get_rate('A', 'C');

	   # get model representation that can be used by Garli
	   my $modelstr	= $model->to_string( '-format' => 'garli' )

DESCRIPTION
       This is a superclass for	models of DNA evolution. Classes that inherit
       from this class provide methods for retreiving general parameters such
       as substitution rates or	the number of states as	well as	model-specific
       parameters. Currently most of the popular models	are implemented. The
       static function "modeltest" determines the substitution model from a
       Bio::Phylo::Matrices::Matrix object and returns the appropriate
       instance	of the subclass. This class also provides serialization	of a
       model to	standard phylogenetics file formats.

METHODS
   CONSTRUCTOR
       new Dna model constructor.

	    Type    : Constructor
	    Title   : new
	    Usage   : my $model	= Bio::Phylo::Models::Substitution::Dna->new(%args);
	    Function: Instantiates a Bio::Phylo::Models::Substitution::Dna object.
	    Returns : A	Bio::Phylo::Models::Substitution::Dna object.
	    Args    : Optional:
			      -type	  => type of model, one	of GTR,	F81, HKY85, JC69, K80
			      -pi	  => base frequencies of bases A, C, G,	T
			      -kappa	  => ratio transitions/transversions
			      -alpha	  => shape parameter (for models of GTR	family)
			      -mu	  => overall mutation rate
			      -pinvar	  => proportion	of invariant sites
			      -ncat	  => number of distinct	rate categories
			      -median	  => median for	gamma-modeled rate categories
			      -rate	  => Array of Arrays (4x4) giving substitution rates betwen A, C, T, G
			      -catweights => weights for rate categories

       get_catrates
	   Getter for rate categories, implemented by child classes.

	    Type    : method
	    Title   : get_catrates
	    Usage   : $model->get_catrates;
	    Function: Getter for rate categories.
	    Returns : scalar or	array
	    Args    : None.

       get_nst
	   Getter for number of	transition rate	parameters.

	    Type    : method
	    Title   : get_nst
	    Usage   : $model->get_nst;
	    Function: Getter for number	of transition rate parameters.
	    Returns : scalar
	    Args    : None.

       get_rate
	   Getter for substitution rate. If bases are given as arguments,
	   returns corresponding rate. If no arguments given, returns rate
	   matrix or overall rate, dependent on	model.

	    Type    : method
	    Title   : get_rate
	    Usage   : $model->get_rate('A', 'C');
	    Function: Getter for transition rate between nucleotides.
	    Returns : scalar or	array
	    Args    : Optional:
		      base1: scalar
		      base2: scalar

       get_nstates
	   Getter for number of	states (bases).

	    Type    : method
	    Title   : get_nstates
	    Usage   : $model->get_nstates;
	    Function: Getter for transition rate between nucleotides.
	    Returns : scalar
	    Args    : None

       get_ncat
	   Getter for number of	rate categories.

	    Type    : method
	    Title   : get_ncat
	    Usage   : $model->get_ncat;
	    Function: Getter for number	of rate	categories.
	    Returns : scalar
	    Args    : None

       get_catweights
	   Getter for weights on rate categories.

	    Type    : method
	    Title   : get_catweights
	    Usage   : $model->get_catweights;
	    Function: Getter for number	of rate	categories.
	    Returns : array
	    Args    : None

       get_kappa
	   Getter for transition/transversion ratio.

	    Type    : method
	    Title   : get_kappa
	    Usage   : $model->get_kappa;
	    Function: Getter for transition/transversion ratio.
	    Returns : scalar
	    Args    : None

       get_alpha
	   Getter for shape parameter.

	    Type    : method
	    Title   : get_alpha
	    Usage   : $model->get_alpha;
	    Function: Getter for shape parameter.
	    Returns : scalar
	    Args    : None

       get_mu
	   Getter for overall mutation rate.

	    Type    : method
	    Title   : get_mu
	    Usage   : $model->get_mu;
	    Function: Getter for overall mutation rate.
	    Returns : scalar
	    Args    : None

       get_pinvar
	   Getter for proportion of invariant sites.

	    Type    : method
	    Title   : get_pinvar
	    Usage   : $model->get_pinvar;
	    Function: Getter for proportion of invariant sites.
	    Returns : scalar
	    Args    : None

       get_pi
	   Getter for base frequencies.

	    Type    : method
	    Title   : get_pi
	    Usage   : $model->get_pi;
	    Function: Getter for base frequencies.
	    Returns : array
	    Args    : Optional:
		      Base (A, C, T or G)

       get_median
	   Getter for median for gamma-modeled rate categories.

	    Type    : method
	    Title   : get_median
	    Usage   : $model->get_median;
	    Function: Getter for median.
	    Returns : scalar
	    Args    : None

       set_rate
	   Setter for substitution rate.

	    Type    : method
	    Title   : set_rate
	    Usage   : $model->set_rate(1);
	    Function: Set nucleotide transition	rates.
	    Returns : A	Bio::Phylo::Models::Substitution::Dna object.
	    Args    : scalar or	array of arrays	(4x4)

       set_ncat
	   Setter for number of	rate categories.

	    Type    : method
	    Title   : set_ncat
	    Usage   : $model->set_ncat(6);
	    Function: Set the number of	rate categoeries.
	    Returns : A	Bio::Phylo::Models::Substitution::Dna object.
	    Args    : scalar

       set_catweights
	   Setter for weights on rate categories.

	    Type    : method
	    Title   : set_catweights
	    Usage   : $model->get_catweights;
	    Function: Set number of rate categories.
	    Returns : A	Bio::Phylo::Models::Substitution::Dna object.
	    Args    : array

       set_kappa
	   Setter for weights on rate categories.

	    Type    : method
	    Title   : set_kappa
	    Usage   : $model->set_kappa(2);
	    Function: Set transition/transversion ratio.
	    Returns : A	Bio::Phylo::Models::Substitution::Dna object.
	    Args    : scalar

       set_alpha
	   Setter for shape parameter.

	    Type    : method
	    Title   : set_alpha
	    Usage   : $model->set_alpha(1);
	    Function: Set shape	parameter.
	    Returns : A	Bio::Phylo::Models::Substitution::Dna object.
	    Args    : scalar

       set_mu
	   Setter for overall mutation rate.

	    Type    : method
	    Title   : set_mu
	    Usage   : $model->set_mu(0.5);
	    Function: Set overall mutation rate.
	    Returns : A	Bio::Phylo::Models::Substitution::Dna object.
	    Args    : scalar

       set_pinvar
	   Set for proportion of invariant sites.

	    Type    : method
	    Title   : set_pinvar
	    Usage   : $model->set_pinvar(0.1);
	    Function: Set proportion of	invariant sites.
	    Returns : A	Bio::Phylo::Models::Substitution::Dna object.
	    Args    : scalar

       set_pi
	   Setter for base frequencies.

	    Type    : method
	    Title   : get_pi
	    Usage   : $model->set_pi((0.2, 0.2,	0.3, 0.3));
	    Function: Set base frequencies.
	    Returns : A	Bio::Phylo::Models::Substitution::Dna object.
	    Args    : array of four base frequencies (A, C, G, T)
	    Comments: Base frequencies must sum	to one

       set_median
	   Setter for median for gamma-modeled rate categories.

	    Type    : method
	    Title   : set_median
	    Usage   : $model->set_median(1);
	    Function: Setter for median.
	    Returns : A	Bio::Phylo::Models::Substitution::Dna object.
	    Args    : scalar

       modeltest
	   Performing a	modeltest using	the package 'phangorn' in R (Schliep,
	   Bioinformatics (2011) 27 (4): 592-593) from an DNA alignment. If no
	   tree	is given as argument, a	neighbor-joining tree is generated
	   from	the alignment to perform model testing.	 Selects the model
	   with	the minimum AIC.

	    Type    : method
	    Title   : modeltest
	    Usage   : $model->modeltest(-matrix=>$matrix);
	    Function: Determine	DNA substitution model from alignment.
	    Returns : An object	which is subclass of Bio::Phylo::Models::Substitution::Dna.
	    Args    : -matrix: A Bio::Phylo::Matrices::Matrix object
		      Optional:
		      -tree: A Bio::Phylo::Forest::Tree	object
		      -timeout:	Timeout	in seconds to prevent getting stuck in an R process.
	    Comments: Prerequisites: Statistics::R, R, and the R package phangorn.

       to_string
	   Get string representation of	model in specified format (paup,
	   phyml, mrbayes or garli)

	    Type    : method
	    Title   : to_string
	    Usage   : $model->to_string(-format=>'mrbayes');
	    Function: Write model to string.
	    Returns : scalar
	    Args    : scalar
	    Comments: format must be either paup, phyml, mrbayes or garli

SEE ALSO
       There is	a mailing list at
       <https://groups.google.com/forum/#!forum/bio-phylo> for any user	or
       developer questions and discussions.

       Bio::Phylo::Manual
	   Also	see the	manual:	Bio::Phylo::Manual and
	   <http://rutgervos.blogspot.com>.

CITATION
       If you use Bio::Phylo in	published research, please cite	it:

       Rutger A	Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase
       Miller, 2011. Bio::Phylo	- phyloinformatic analysis using Perl.	BMC
       Bioinformatics 12:63.  <http://dx.doi.org/10.1186/1471-2105-12-63>

perl v5.32.0			  2017Bio::Phylo::Models::Substitution::Dna(3)

NAME | SYNOPSIS | DESCRIPTION | METHODS | SEE ALSO | CITATION

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