seq::NucleotideSubstitutionModel Class Reference

Describes the mutation behaviour of (the whole of) replication enzymes for one replication cycle. More...

#include <NucleotideSubstitutionModel.h>

List of all members.

Public Member Functions
	NucleotideSubstitutionModel (double piA, double piC, double piG, double piT, double rAC, double rAG, double rAT, double rCG, double rCT, double rGT, double errorRate)
	Construct a stationary substitution model based on:.
	NucleotideSubstitutionModel (double rAC, double rAG, double rAT, double rCA, double rCG, double rCT, double rGA, double rGC, double rGT, double rTA, double rTC, double rTG, double piA, double piC, double piG, double piT, double errorRate)
	Construct a (non-stationary) substitution model based on:.
double	getMu (Nucleotide fromNT, Nucleotide toNT) const
	Retrieve average rate of copying a nucleotide into a particular other nucleotide.
void	print (std::ostream &s) const

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Detailed Description

Describes the mutation behaviour of (the whole of) replication enzymes for one replication cycle.

In particular, it models the nucleotide-dependent error rate behaviour of the enzyme.

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Constructor & Destructor Documentation

seq::NucleotideSubstitutionModel::NucleotideSubstitutionModel (  double  piA, double  piC, double  piG, double  piT, double  rAC, double  rAG, double  rAT, double  rCG, double  rCT, double  rGT, double  errorRate )

Construct a stationary substitution model based on:. the 4 stationary nucleotide frequencies the (relative) 6 symmetrical substitution rates. the average error rate per generation per site (mu)

seq::NucleotideSubstitutionModel::NucleotideSubstitutionModel (  double  rAC, double  rAG, double  rAT, double  rCA, double  rCG, double  rCT, double  rGA, double  rGC, double  rGT, double  rTA, double  rTC, double  rTG, double  piA, double  piC, double  piG, double  piT, double  errorRate )

Construct a (non-stationary) substitution model based on:. the 12 relative substitution rates the 4 stationary nucleotide frequencies used to calibrate the average error rate per generation per site the average error rate per generation per site

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Member Function Documentation

double seq::NucleotideSubstitutionModel::getMu (  Nucleotide  fromNT, Nucleotide  toNT )  const

Retrieve average rate of copying a nucleotide into a particular other nucleotide. Returns: the error rate in nucleotide changes per replication cycle

void seq::NucleotideSubstitutionModel::print (  std::ostream &  s  )  const

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The documentation for this class was generated from the following files:

• src/evolution/NucleotideSubstitutionModel.h
• src/evolution/NucleotideSubstitutionModel.C

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