net.maizegenetics.taxa.tree

Class NeighborJoiningTree

java.lang.Object

net.maizegenetics.taxa.tree.SimpleTree

net.maizegenetics.taxa.tree.NeighborJoiningTree

All Implemented Interfaces:

Serializable, Tree, Units, UnitsProvider

public class NeighborJoiningTree
extends SimpleTree

constructs a neighbor-joining tree from pairwise distances

Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol, 4(4):406-425,

Author:

Korbinian Strimmer, Alexei Drummond

See Also:

Serialized Form

Field Summary

Fields inherited from interface net.maizegenetics.taxa.tree.Units

DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS

Constructor Summary

Constructors

Constructor and Description
NeighborJoiningTree(DistanceMatrix m) construct NJ tree

Method Summary

Methods inherited from class net.maizegenetics.taxa.tree.SimpleTree

createNodeList, findNode, getAttribute, getCopy, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, report, reroot, reroot, setAttribute, setRoot, setUnits, toString, whichIdNumber

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

NeighborJoiningTree

public NeighborJoiningTree(DistanceMatrix m)

construct NJ tree

Parameters:

m - distance matrix