Class | Description |
---|---|
pal.tree.UPGMATree |
Use ClusterTree
|
Method | Description |
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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()
|