the bioinformatics chat

A podcast about computational biology, bioinformatics, and next generation sequencing.


episode 55: Phylogenetics and the likelihood gradient with Xiang Ji

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.


  • 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


 2021-01-13  57m