the bioinformatics chat

#55 Phylogenetics and the likelihood gradient with Xiang Ji

Listen Later

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:

  • 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

    • If you enjoyed this episode, please consider supporting the podcast on Patreon.

    ...more
    View all episodesView all episodes
    Download on the App Store
    the bioinformatics chatBy Roman Cheplyaka
    • 4.8
    • 4.8
    • 4.8
    • 4.8
    • 4.8

    4.8

    34 ratings

    More shows like the bioinformatics chat

    View all
    Radiolab by WNYC Studios

    Radiolab

    43,909 Listeners

    This American Life by This American Life

    This American Life

    90,830 Listeners

    The Bioinformatics and Beyond Podcast by Leo Elworth

    The Bioinformatics and Beyond Podcast

    10 Listeners

    If Books Could Kill by Michael Hobbes & Peter Shamshiri

    If Books Could Kill

    8,747 Listeners

    the bioinformatics lab by The Bioinformatics Lab

    the bioinformatics lab

    0 Listeners