Package pal.supgma
Class SUPGMATree
java.lang.Object
pal.tree.SimpleTree
pal.tree.ClusterTree
pal.supgma.SUPGMATree
- All Implemented Interfaces:
Serializable
,IdGroup
,Report
,Units
,UnitsProvider
,Tree
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
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:
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Nested Class Summary
Nested classes/interfaces inherited from class pal.tree.ClusterTree
ClusterTree.ClusteringMethod
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
Nested classes/interfaces inherited from interface pal.tree.Tree
Tree.TreeBase
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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
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Constructor Summary
ConstructorsConstructorDescriptionSUPGMATree
(DistanceMatrix m, TimeOrderCharacterData tocd, double rate, ClusterTree.ClusteringMethod cm) constructor SUPGMA treeSUPGMATree
(DistanceMatrix m, TimeOrderCharacterData tocd, DeltaModel deltaModel, boolean allowNegatives, 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
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Constructor Details
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SUPGMATree
public SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, double rate, ClusterTree.ClusteringMethod cm) constructor SUPGMA tree- Parameters:
m
- *uncorrected* distance matrix
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SUPGMATree
public SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, DeltaModel deltaModel, boolean allowNegatives, ClusterTree.ClusteringMethod cm) constructor SUPGMA tree- Parameters:
m
- *uncorrected* distance matrix
-