Class PhylogenyMath

java.lang.Object

org.episteme.natural.biology.phylogeny.PhylogenyMath

public class PhylogenyMath
extends Object

Basic phylogenetics utilities and mathematical models.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

Constructor Summary

Constructors

Constructor	Description
PhylogenyMath()

Method Summary

Modifier and Type	Method	Description
static Real[][]	calculateDistanceMatrix(List<String> sequences)	Calculates distance matrix from a list of aligned sequences.
static Real	jukesCantorDistance(Real pDistance)	Jukes-Cantor distance correction. d_JC = -3/4 * ln(1 - 4/3 * p)
static Real	pDistance(String s1, String s2)	p-distance: proportion of nucleotide sites that are different. d = n_d / n

Methods inherited from class Object

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

Constructor Details

PhylogenyMath

public PhylogenyMath()

Method Details

calculateDistanceMatrix

public static Real[][] calculateDistanceMatrix(List<String> sequences)

Calculates distance matrix from a list of aligned sequences. Using simple Hamming distance (p-distance).

Parameters:

sequences - List of aligned DNA strings (same length)

Returns:

Symmetric distance matrix

pDistance

public static Real pDistance(String s1,
 String s2)

p-distance: proportion of nucleotide sites that are different. d = n_d / n

jukesCantorDistance

public static Real jukesCantorDistance(Real pDistance)

Jukes-Cantor distance correction. d_JC = -3/4 * ln(1 - 4/3 * p)