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arXiv · 2008.07054

An empirical guide for producing a dated phylogeny with treePL in a maximum likelihood framework

Kévin J. L. Maurin
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Abstract

treePL uses a penalised likelihood approach to produce a dated phylogeny in a maximum likelihood framework. Since its publication in 2012, few resources have been developed to explain how to use it properly. In this guide, I provide a step-by-step protocol for producing a dated phylogeny using treePL, based on my experience building a large dated phylogeny with it and conducting additional tests on a smaller phylogeny. I also provide the necessary data to reproduce one of the example phylogenies presented. I compare these treePL phylogenies to BEAST2-built counterparts. Even though I cannot explain precisely how treePL works, the evidence discussed in this guide suggest that the empirical protocol presented is reliable.

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Kévin J. L. Maurin. 2020-08-17. An empirical guide for producing a dated phylogeny with treePL in a maximum likelihood framework. https://arxiv.org/abs/2008.07054

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