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