Sequence::Kimura80 Class Reference
[Divergence Statistics]

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

#include <Sequence/Kimura80.hpp>

List of all members.

Public Member Functions
	Kimura80 (const Sequence::Seq *seqa, const Sequence::Seq *seqb)
double	K ()
size_t	sites (void)

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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.

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Constructor & Destructor Documentation

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:

Sequence::SeqException

if sequences are of different lengths

Definition at line 47 of file Kimura80.cc.

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Member Function Documentation

double Sequence::Kimura80::K

(

void

)

Returns:

the distance between the two sequences.

Note:

999.0 is returned as a warning value. This can be necessary if sites are saturated, which implies that divergence cannot be calculated

Definition at line 116 of file Kimura80.cc.

size_t Sequence::Kimura80::sites

(

void

)

Returns:

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

Definition at line 130 of file Kimura80.cc.

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

• Kimura80.hpp
• Kimura80.cc