edu.rit.compbio.phyl
Class JukesCantorDistance

java.lang.Object
  edu.rit.compbio.phyl.JukesCantorDistance

All Implemented Interfaces:

Distance

public class JukesCantorDistance
extends Object
implements Distance

Class JukesCantorDistance provides an object that computes the Jukes-Cantor distance between two DnaSequences. This is the corrected distance under the Jukes-Cantor model of DNA sequence evolution. The formula is

D_JC = −3/4 N ln (1 − 4/3 D_H/N) where D_JC is the Jukes-Cantor distance, D_H is the Hamming distance (number of differing sites), and N is the number of sites. For further information, see:

• T. Jukes and C. Cantor. Evolution of protein molecules. In M. Munro, editor. Mammalian Protein Metabolism, Volume III. Academic Press, 1969, pages 21-132.
• J. Felsenstein. Inferring Phylogenies. Sinauer Associates, 2004, pages 156-158.

Constructor Summary

JukesCantorDistance()
Construct a new Jukes-Cantor distance object.

Method Summary

double

distance(DnaSequence seq1, DnaSequence seq2) Compute the distance between the two given DNA sequences.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

JukesCantorDistance

public JukesCantorDistance()

Construct a new Jukes-Cantor distance object.

Method Detail

distance

public double distance(DnaSequence seq1,
                       DnaSequence seq2)

Compute the distance between the two given DNA sequences. It is assumed that the DNA sequences are the same length.

Specified by:

distance in interface Distance

Parameters:

seq1 - First DNA sequence.

seq2 - Second DNA sequence.

Returns:

Distance.