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 | |
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 and Description |
---|---|
static DistanceMatrixGenerator |
DistanceMatrixGenerator.Utils.createEvolutionary(Alignment a,
SubstitutionModel sm) |
static DistanceMatrixGenerator |
DistanceMatrixGenerator.Utils.createParametric(Tree baseTree,
SubstitutionModel sm,
int numberOfSites)
Silly idea stuff
|
Modifier and Type | Method and Description |
---|---|
Tree |
SUPGMABase.PopulationParameters.generateSUPGMATree(AlgorithmCallback callback,
ClusterTree.ClusteringMethod cm,
DistanceMatrixGenerator replicateSource,
int numberOfAlignmentBootstrapReplicates,
LMSSolver solver) |
Constructor and Description |
---|
SUPGMABase(DistanceMatrixAccess distanceAccess,
DistanceMatrixGenerator replicateGenerator,
TimeOrderCharacterData tocd) |
Modifier and Type | Method and Description |
---|---|
static TreeGenerator |
TreeGenerator.Utils.createNeighbourJoiningGenerator(DistanceMatrixGenerator dataGenerator,
java.lang.String[] outgroupNames) |