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.
@article{arxiv.2008.07054,
title = {An empirical guide for producing a dated phylogeny with treePL in a maximum likelihood framework},
author = {Kévin J. L. Maurin},
journal= {arXiv preprint arXiv:2008.07054},
year = {2020}
}
Comments
11 pages, 3 figures, supplementary material available at https://doi.org/10.5281/zenodo.3989030