Coalescent Hidden Markov Model

COALESCENT HIDDEN MARKOV MODEL. Cupressus sempervirens, Italian cypress.
600 block of Mayfield Avenue, facing east.

Coalescent-based hidden Markov models move along the genome, describing the ancestral process for a set of sampled sequences at each of a series of genomic locations. In particular, a coalescent HMM keeps track of the tree height at each genomic segment; tree heights at neighboring sites are correlated, and the tree height can have discontinuous changes at points where recombination has occurred.