Class PhylogeneticTree

java.lang.Object

org.episteme.natural.biology.phylogeny.PhylogeneticTree

public class PhylogeneticTree
extends Object

Phylogenetic tree construction and representation.

Supports multiple tree construction algorithms:

• UPGMA (Unweighted Pair Group Method with Arithmetic Mean)
• Neighbor-Joining

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PhylogeneticTree.Node	Node in a phylogenetic tree with branch length support.

Constructor Summary

Constructors

Constructor	Description
PhylogeneticTree()

Method Summary

Modifier and Type	Method	Description
static Tree<PhylogeneticTree.Node>	asTree(PhylogeneticTree.Node root)	Converts a phylogenetic tree to a Tree interface for graph operations.
static PhylogeneticTree.Node	buildNeighborJoining(Real[][] distanceMatrix, List<Species> speciesList)
static PhylogeneticTree.Node	buildNeighborJoiningFromLabels(Real[][] distanceMatrix, List<String> labels)	Builds a phylogenetic tree using Neighbor-Joining algorithm (String labels).
static PhylogeneticTree.Node	buildUPGMA(Real[][] distanceMatrix, List<Species> speciesList)
static PhylogeneticTree.Node	buildUPGMAFromLabels(Real[][] distanceMatrix, List<String> labels)	Builds a phylogenetic tree using UPGMA algorithm (String labels).
static int	countLeaves(PhylogeneticTree.Node node)	Counts the number of leaves in the tree.
static List<String>	getLeafNames(PhylogeneticTree.Node node)	Gets all leaf names from the tree.
static PhylogeneticTree.Node	parseNewick(String newick)	Parses a Newick format string into a phylogenetic tree.

Methods inherited from class Object

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

Constructor Details

PhylogeneticTree

public PhylogeneticTree()

Method Details

buildUPGMA

public static PhylogeneticTree.Node buildUPGMA(Real[][] distanceMatrix,
 List<Species> speciesList)

buildUPGMAFromLabels

public static PhylogeneticTree.Node buildUPGMAFromLabels(Real[][] distanceMatrix,
 List<String> labels)

Builds a phylogenetic tree using UPGMA algorithm (String labels).

buildNeighborJoining

public static PhylogeneticTree.Node buildNeighborJoining(Real[][] distanceMatrix,
 List<Species> speciesList)

buildNeighborJoiningFromLabels

public static PhylogeneticTree.Node buildNeighborJoiningFromLabels(Real[][] distanceMatrix,
 List<String> labels)

Builds a phylogenetic tree using Neighbor-Joining algorithm (String labels).

asTree

public static Tree<PhylogeneticTree.Node> asTree(PhylogeneticTree.Node root)

Converts a phylogenetic tree to a Tree interface for graph operations.

Parameters:

root - the root node

Returns:

a Tree implementation

parseNewick

public static PhylogeneticTree.Node parseNewick(String newick)

Parses a Newick format string into a phylogenetic tree.

Parameters:

newick - the Newick format string

Returns:

root node of the parsed tree

countLeaves

public static int countLeaves(PhylogeneticTree.Node node)

Counts the number of leaves in the tree.

getLeafNames

public static List<String> getLeafNames(PhylogeneticTree.Node node)

Gets all leaf names from the tree.