localClock(TimeTree tree, Object[] clades, Double[] cladeRates, Double rootRate, Boolean includeStem)

Apply local clock in a phylogenetic tree to generate a tree with branch rates. The order of elements in clades and cladeRates array should match. The clades should not be overlapped with each other.

Parameters

  • TimeTree tree - the tree used to calculate branch rates
  • Object[] clades - the array of the node names
  • Double[] cladeRates - the array of clade rates
  • Double rootRate - the root rate of the tree
  • Boolean includeStem - (optional) whether to include stem of clades, defaults to true

Return type

Double[]

Examples

  • substituteClade.lphy