Kimura's 2-parameter distance. More...

#include <Sequence/Kimura80.hpp>

Public Member Functions
	Kimura80 (const Sequence::Seq seqa, const Sequence::Seq seqb)

double	K () const

size_t	sites (void) const

Detailed Description

Kimura's 2-parameter distance.

Calculate a measure of sequence divergence using Kimura's 1980 method.
The reference is: Kimura, M (1980) J. Mol. Evol 16: 111-120.
The calculation only depends on 3 numbers:
1.) the number of sites in the sequence
2.) the number of transitions between the two sequences
3.) the number of transversions between the two sequences

The implementation of this class does the following:
1.) compare each position in both sequences, counting transitions and transversions
2.) calculate distance using Kimura's formula

Exceptions

Sequence::SeqException if the two sequences are of unequal length.

Definition at line 51 of file Kimura80.hpp.

Constructor & Destructor Documentation

◆ Kimura80()

Sequence::Kimura80::Kimura80	(	const Sequence::Seq *	seqa,
		const Sequence::Seq *	seqb
	)

explicit

Parameters

seqa	an object of type Sequence::Seq
seqb	an object of type Sequence::Seq

Exceptions

std::runtime_error if sequences are of different lengths

Definition at line 41 of file Kimura80.cc.

Member Function Documentation

◆ K()

double Sequence::Kimura80::K ( void ) const

Returns: the distance between the two sequences.

Note: non-signaling nan is returned as a warning value. This can be necessary if sites are saturated, which implies that divergence cannot be calculated

Definition at line 109 of file Kimura80.cc.

◆ sites()

size_t Sequence::Kimura80::sites ( void ) const

Returns: the number of sites compared, excluding gaps, missing data, etc.

Definition at line 123 of file Kimura80.cc.