jebl.evolution.align.scores
Class JukesCantor

java.lang.Object
  jebl.evolution.align.scores.Scores
      jebl.evolution.align.scores.NucleotideScores
          jebl.evolution.align.scores.JukesCantor

All Implemented Interfaces:

ScoreMatrix

public class JukesCantor
extends NucleotideScores

Jukes Cantor assumes equal substitution frequencies and equal nucleotide equilibrium frequencies.

Author:

Richard Moir

Field Summary

Fields inherited from class jebl.evolution.align.scores.NucleotideScores

CLUSTALW, IUB

Fields inherited from class jebl.evolution.align.scores.Scores

score

Constructor Summary

JukesCantor(float d)

Method Summary

Methods inherited from class jebl.evolution.align.scores.NucleotideScores

getAlphabet, getName, toString

Methods inherited from class jebl.evolution.align.scores.Scores

buildScores, duplicate, getExtraResidues, getScore, includeAdditionalCharacters, includeGaps

Methods inherited from class java.lang.Object

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

Constructor Detail

JukesCantor

public JukesCantor(float d)

Parameters:

d - evolutionary distance used to calculate values