Package | Description |
---|---|
pal.supgma | |
pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
Modifier and Type | Method | Description |
---|---|---|
Tree |
SUPGMABase.generateAlignmentBootstrappedSUPGMATree(AlgorithmCallback callback,
ClusterTree.ClusteringMethod cm,
SUPGMABase.PopulationParameters pp,
int numberOfReplicates,
LMSSolver solver) |
|
Tree |
SUPGMABase.PopulationParameters.generateSUPGMATree(ClusterTree.ClusteringMethod cm) |
|
Tree |
SUPGMABase.PopulationParameters.generateSUPGMATree(AlgorithmCallback callback,
ClusterTree.ClusteringMethod cm,
DistanceMatrixGenerator replicateSource,
int numberOfAlignmentBootstrapReplicates,
LMSSolver solver) |
|
Tree |
SUPGMABase.solve(AlgorithmCallback callback,
ClusterTree.ClusteringMethod cm,
LMSSolver solver) |
Constructor | Description |
---|---|
SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
double rate,
ClusterTree.ClusteringMethod cm) |
constructor SUPGMA tree
|
SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
DeltaModel deltaModel,
boolean allowNegatives,
ClusterTree.ClusteringMethod cm) |
constructor SUPGMA tree
|
Modifier and Type | Field | Description |
---|---|---|
static ClusterTree.ClusteringMethod |
ClusterTree.COMPLETE_LINKAGE |
|
static ClusterTree.ClusteringMethod |
ClusterTree.SINGLE_LINKAGE |
|
static ClusterTree.ClusteringMethod |
ClusterTree.UPGMA |
|
static ClusterTree.ClusteringMethod |
ClusterTree.WPGMA |
Constructor | Description |
---|---|
ClusterTree(DistanceMatrix dm,
ClusterTree.ClusteringMethod cm) |