pal.tree
Class SUPGMATree
java.lang.Object
|
+--pal.tree.SimpleTree
|
+--pal.tree.UPGMATree
|
+--pal.tree.SUPGMATree
- All Implemented Interfaces:
- Report, java.io.Serializable, Tree, Units
- public class SUPGMATree
- extends UPGMATree
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
- See Also:
- Serialized Form
Methods inherited from class pal.tree.SimpleTree |
createNodeList, findNode, getAttribute, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, report, reroot, reroot, setAttribute, setRoot, setUnits, toString |
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)
- constructor SUPGMA tree
- Parameters:
m
- *uncorrected* distance matrix
SUPGMATree
public SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
double rate,
boolean allowNegatives)
- constructor SUPGMA tree
- Parameters:
m
- *uncorrected* distance matrix
getDatedTipsClockTree
public DatedTipsClockTree getDatedTipsClockTree()