Package pal.tree
Class NeighborJoiningTree
- java.lang.Object
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- pal.tree.SimpleTree
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- pal.tree.NeighborJoiningTree
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- All Implemented Interfaces:
java.io.Serializable
,IdGroup
,Report
,Units
,UnitsProvider
,Tree
public class NeighborJoiningTree extends SimpleTree
constructs a neighbor-joining tree from pairwise distances
Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol, 4(4):406-425,- Version:
- $Id: NeighborJoiningTree.java,v 1.12 2003/09/16 03:54:18 matt Exp $
- Author:
- Korbinian Strimmer, Alexei Drummond
- See Also:
- Serialized Form
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Nested Class Summary
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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 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 NeighborJoiningTree(DistanceMatrix m)
construct NJ 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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NeighborJoiningTree
public NeighborJoiningTree(DistanceMatrix m)
construct NJ tree- Parameters:
m
- distance matrix
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