Coalescent(Number theta, Integer n, Taxa taxa, Double[] ages)

The Kingman coalescent with serially sampled data. (Rodrigo and Felsenstein, 1999)

Parameters

  • Number theta - effective population size, possibly scaled to mutations or calendar units.
  • Integer n - (optional) number of taxa.
  • Taxa taxa - (optional) Taxa object, (e.g. Taxa or TimeTree or Object[])
  • Double[] ages - (optional) an array of leaf node ages.

Return type

TimeTree

Examples

  • https://linguaphylo.github.io/tutorials/time-stamped-data/

Reference

Rodrigo AG, Felsenstein J. (1999). Coalescent Approaches to HIV Population Genetics, The Evolution of HIV, Chapter 8, edited by Crandall K., Johns Hopkins Univ. Press, Baltimore.