Package pal.supgma
Class SUPGMATree
- java.lang.Object
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- pal.tree.SimpleTree
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- pal.tree.ClusterTree
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- pal.supgma.SUPGMATree
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from class pal.tree.ClusterTree
ClusterTree.ClusteringMethod
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Nested classes/interfaces inherited from interface pal.tree.Tree
Tree.TreeBase
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Field Summary
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Fields inherited from class pal.tree.ClusterTree
COMPLETE_LINKAGE, SINGLE_LINKAGE, UPGMA, WPGMA
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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
Constructors Constructor Description SUPGMATree(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
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Method Summary
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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 Detail
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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
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