Xiang Ji's guest appearances

Xiang Ji

the bioinformatics chat

David Kelley

Irineo Cabreros

Romain Lopez

Gabriel Misrachi

Hassan Samee

Kristina Grigaityte

Jacob Schreiber

Simeon Carstens

Trevor Pesout

HoJoon Lee

Seung Woo Cho

Kaushik Panda

Keith Slotkin

Fernando Portela

Chang Xu

OwlTail

In this episode, we chat about phylogenetics with Xiang Ji. We start with ageneral 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  If you enjoyed this episode, please consider supporting the podcast on Patreon!

In this episode, we chat about phylogenetics with <a href="http://xiang-ji-ncsu.github.io/" rel="nofollow" target="_blank">Xiang Ji</a>. 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: <ul> <li><a href="https://academic.oup.com/mbe/article/37/10/3047/5847600" rel="nofollow" target="_blank">Gradients Do Grow on Trees: A Linear-Time O(N)-Dimensional Gradient for Statistical Phylogenetics</a> (Xiang Ji, Zhenyu Zhang, Andrew Holbrook, Akihiko Nishimura, Guy Baele, Andrew Rambaut, Philippe Lemey, Marc A Suchard)</li> <li><a href="https://github.com/beagle-dev/beagle-lib" rel="nofollow" target="_blank">BEAGLE</a>: the package that implements the gradient algorithm</li> <li><a href="http://beast.community/" rel="nofollow" target="_blank">BEAST</a>: the program that implements the Hamiltonian Monte Carlo sampler and the molecular clock models</li> </ul> If you enjoyed this episode, please consider supporting the podcast on <a href="https://www.patreon.com/bioinfochat" rel="nofollow" target="_blank">Patreon</a>!

#55 Phylogenetics and the likelihood gradient with Xiang Ji