pal.tree
Class NeighborJoiningTree

java.lang.Object
  extended by pal.tree.SimpleTree
      extended by pal.tree.NeighborJoiningTree
All Implemented Interfaces:
java.io.Serializable, IdGroup, Report, Units, UnitsProvider, Tree

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,

Version:
$Id: NeighborJoiningTree.java,v 1.12 2003/09/16 03:54:18 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface pal.tree.Tree
Tree.TreeBase
 
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
 
Field Summary
 
Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
 
Constructor Summary
NeighborJoiningTree(DistanceMatrix m)
          construct NJ tree
 
Method Summary
 
Methods inherited from class pal.tree.SimpleTree
createNodeList, findNode, getAttribute, getCopy, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getRoot, getUnits, report, reroot, reroot, setAttribute, setIdentifier, setRoot, setUnits, toString, whichIdNumber
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

NeighborJoiningTree

public NeighborJoiningTree(DistanceMatrix m)
construct NJ tree

Parameters:
m - distance matrix