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

Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, YEARS
 
Constructor Summary
SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, double rate)
          constructor SUPGMA tree
SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, double rate, boolean allowNegatives)
          constructor SUPGMA tree
 
Method Summary
 DatedTipsClockTree getDatedTipsClockTree()
           
 
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
 

Constructor Detail

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
Method Detail

getDatedTipsClockTree

public DatedTipsClockTree getDatedTipsClockTree()