NeighborJoiningTree

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Summary:
Nested |
Field |
Constr |
Method

Detail:
Field |
Constr |
Method

java.lang.Object
- pal.tree.SimpleTree
- - 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.misc.IdGroup
    IdGroup.Utils
  - Nested classes/interfaces inherited from interface pal.tree.Tree
    Tree.TreeBase
- Field Summary
  - Fields inherited from interface pal.misc.Units
    DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
- Constructor Summary
  
  Constructors
  Constructor Description
  
  NeighborJoiningTree(DistanceMatrix m)
  construct NJ tree
- Method Summary
  - Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
  - 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

- Constructor Detail
  - NeighborJoiningTree
```
public NeighborJoiningTree(DistanceMatrix m)
```
    construct NJ tree
    
    Parameters:
    
    m - distance matrix

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