pal.supgma
Class 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
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 |
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