| Package | Description |
|---|---|
| pal.distance |
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
|
| pal.supgma |
| Modifier and Type | Method | Description |
|---|---|---|
static DistanceMatrixAccess |
DistanceMatrixAccess.Utils.createEvolutionary(Alignment a,
SubstitutionModel sm) |
|
static DistanceMatrixAccess |
DistanceMatrixAccess.Utils.createSimple(DistanceMatrix base) |
| Modifier and Type | Method | Description |
|---|---|---|
SUPGMABase.PopulationParameters |
SUPGMABase.process(DistanceMatrixAccess alternativeSource,
AlgorithmCallback callback,
LMSSolver solver) |
| Constructor | Description |
|---|---|
SUPGMABase(DistanceMatrixAccess distanceAccess,
DistanceMatrixGenerator replicateGenerator,
TimeOrderCharacterData tocd) |