SUPGMATree

java.lang.Object
- pal.tree.SimpleTree
- - pal.tree.ClusterTree
  - - pal.supgma.SUPGMATree

All Implemented Interfaces:

java.io.Serializable, IdGroup, Report, Units, UnitsProvider, Tree
```
public class SUPGMATree
extends ClusterTree
```
constructs an SUPGMA tree from pairwise distances.
Reference:
Alexei Drummond and Allen G. Rodrigo (2000). Reconstructing Genealogies of Serial Samples Under the Assumption of a Molecular Clock Using Serial-Sample UPGMA. Molecular Biology and Evolution 17:1807-1815

Version:

$Id: SUPGMATree.java,v 1.1 2003/10/19 02:35:26 matt Exp $

Author:

Alexei Drummond, Matthew Goode

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class pal.tree.ClusterTree
  ClusterTree.ClusteringMethod
- 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 class pal.tree.ClusterTree
  COMPLETE_LINKAGE, SINGLE_LINKAGE, UPGMA, WPGMA
- Fields inherited from interface pal.misc.Units
  DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS

Constructor Summary

Constructors
Constructor and Description
`SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, DeltaModel deltaModel, boolean allowNegatives, ClusterTree.ClusteringMethod cm)` constructor SUPGMA tree
`SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, double rate, ClusterTree.ClusteringMethod cm)` constructor SUPGMA 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

SUPGMATree

public SUPGMATree(DistanceMatrix m,
                  TimeOrderCharacterData tocd,
                  double rate,
                  ClusterTree.ClusteringMethod cm)

constructor SUPGMA tree

Parameters:: m - *uncorrected* distance matrix

SUPGMATree

public SUPGMATree(DistanceMatrix m,
                  TimeOrderCharacterData tocd,
                  DeltaModel deltaModel,
                  boolean allowNegatives,
                  ClusterTree.ClusteringMethod cm)

constructor SUPGMA tree

Parameters:: m - *uncorrected* distance matrix

Class SUPGMATree

Nested Class Summary

Nested classes/interfaces inherited from class pal.tree.ClusterTree

Nested classes/interfaces inherited from interface pal.tree.Tree

Nested classes/interfaces inherited from interface pal.misc.IdGroup

Field Summary

Fields inherited from class pal.tree.ClusterTree

Fields inherited from interface pal.misc.Units

Constructor Summary

Method Summary

Methods inherited from class pal.tree.SimpleTree

Methods inherited from class java.lang.Object

Constructor Detail

SUPGMATree

SUPGMATree