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bioRxiv · 10.1101/2022.12.21.521328

CherryML: Scalable Maximum Likelihood Estimation of Phylogenetic Models

Prillo, S.·Deng, Y.·Boyeau, P.·Li, X.·Chen, P.-Y.·Song, Y. S.
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Abstract

Phylogenetic models of molecular evolution are central to diverse problems in biology, but maximum likelihood estimation of model parameters is a computationally expensive task, in some cases prohibitively so. To address this challenge, we here introduce CherryML, a broadly applicable method that achieves several orders of magnitude speedup. We demonstrate its utility by applying it to estimate a general 400 x 400 rate matrix for amino acid co-evolution at protein contact sites.

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Prillo, S., Deng, Y., Boyeau, P., Li, X., Chen, P.-Y., Song, Y. S.. 2022-12-22. CherryML: Scalable Maximum Likelihood Estimation of Phylogenetic Models. https://doi.org/10.1101/2022.12.21.521328

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