In this episode, we chat about phylogenetics with Xiang Ji. We start with a

general introduction to the field and then go deeper into the likelihood-based

methods (maximum likelihood and Bayesian inference). In particular, we talk

about the different ways to calculate the likelihood gradient, including a

linear-time exact gradient algorithm recently published by Xiang and his

colleagues.

Links:

BEAGLE: the package that implements the gradient algorithm

BEAST: the program that implements the Hamiltonian Monte Carlo sampler and the molecular clock models

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