Uses of Interface
pal.mep.DeltaModel

Packages that use DeltaModel

pal.mep	Classes for the analysis of "measurably evolving populations" (mep).
pal.supgma

Uses of DeltaModel in pal.mep

Methods in pal.mep that return DeltaModel

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 models
static 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

static DeltaModel

DeltaModel.Utils.getDisjointBased(DeltaModel primaryModel, DeltaModel subgroupModel, TimeOrderCharacterData subgroupTOCD)

Uses of DeltaModel in pal.supgma

Constructors in pal.supgma with parameters of type DeltaModel

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