| Class and Description |
|---|
| pal.tree.UPGMATree
Use ClusterTree
|
| Method and Description |
|---|
| pal.misc.Utils.argmax(double[]) |
| pal.misc.Utils.argmax(int[]) |
| pal.tree.TreeUtils.getBootstrapSupportByCladeTree(String, Tree, Tree[])
Use getReplicateCladeSupport instead
|
| pal.distance.DistanceMatrix.getIdGroup()
distance matrix now implements IdGroup
|
| pal.misc.TimeOrderCharacterData.getIdGroup()
TimeOrderCharacterData now implements IdGroup
|
| pal.substmodel.RateMatrix.getRelativeRates()
try not to use.
|
| pal.misc.TimeOrderCharacterData.getSampleCount()
Use getOrdinalCount()
|
| pal.datatype.DataType.Utils.isGap(DataType, char)
use DataType.isGapChar()
|
| pal.tree.TreeUtils.scale(Tree, double, int)
use getScaled()
|
| pal.tree.TreeUtils.scale(Tree, MutationRateModel)
use getScaled()
|
| pal.tree.TreeUtils.scale(Tree, MutationRateModel, int)
use getScaled()
|