Package | Description |
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pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
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pal.supgma |
Modifier and Type | Method | Description |
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static DeltaModel |
DeltaModel.Utils.getDisjointBased(DeltaModel primaryModel,
DeltaModel subgroupModel,
TimeOrderCharacterData subgroupTOCD) |
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static DeltaModel |
DeltaModel.Utils.getMutationRateModelBased(MutationRateModel.Factory mepFactory) |
For interfacing with time based mutation rate models
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static DeltaModel |
DeltaModel.Utils.getUntimedBased() |
For serial sampled analysis when no time information is available.
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static DeltaModel |
DeltaModel.Utils.getUntimedBased(double[] initalDeltas) |
For serial sampled analysis when no time information is available.
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Modifier and Type | Method | Description |
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static DeltaModel |
DeltaModel.Utils.getDisjointBased(DeltaModel primaryModel,
DeltaModel subgroupModel,
TimeOrderCharacterData subgroupTOCD) |
Constructor | Description |
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SUPGMADistanceMatrix(DistanceMatrix raw,
TimeOrderCharacterData tocd,
DeltaModel deltaModel) |
Uses date/time information and a constant rate to correct distance matrices.
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SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
DeltaModel deltaModel,
boolean allowNegatives,
ClusterTree.ClusteringMethod cm) |
constructor SUPGMA tree
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