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-basedmethods (maximum likelihood and Bayesian inference). In particular, we talkabout the different ways to calculate the likelihood gradient, including alinear-time exact gradient algorithm recently published by Xiang and hiscolleagues.

Links:

• Gradients Do Grow on Trees: A Linear-Time O(N)-Dimensional Gradient for Statistical Phylogenetics
  (Xiang Ji, Zhenyu Zhang, Andrew Holbrook, Akihiko Nishimura, Guy Baele, Andrew Rambaut, Philippe Lemey, Marc A Suchard)
• BEAGLE: the package that implements the gradient algorithm
• BEAST: the program that implements the Hamiltonian Monte Carlo sampler and the molecular clock models