Vu Dinh, Arman Bilge, Cheng Zhang, and Frederick A Matsen IV. Probabilistic path Hamiltonian Monte Carlo. In Proceedings of the 34th International Conference on Machine Learning, pp. 1009-1018, July 2017. URL http://proceedings.mlr.press/v70/dinh17a.html.
Vu C. Dinh, Aaron E. Darling, and Frederick A. Matsen IV. Online Bayesian phylogenetic inference: Theoretical foundations via sequential Monte Carlo. Systematic Biology, 67:503 - 517, 2016.
Louis du Plessis, John T McCrone, Alexander E Zarebski, Verity Hill, Christopher Ruis, Bernardo Gutierrez, Jayna Raghwani, Jordan Ashworth, Rachel Colquhoun, Thomas R Connor, Nuno R Faria, Ben Jackson, Nicholas J Loman, Aine O'Toole, Samuel M Nicholls, Kris V Parag, Emily Scher, Tetyana I Vasylyeva, Erik M Volz, Alexander Watts, Isaac I Bogoch, Kamran Khan, COVID-19 Genomics UK (COG-UK) Consortium†, David M Aanensen, Moritz U G Kraemer, Andrew Rambaut, and Oliver G Pybus. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science, January 2021. ISSN 0036-8075, 1095-9203. doi: 10.1126/science.abf2946. URL https://science.sciencemag.org/content/early/2021/01/07/science.abf2946.
Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J Tatem, Guy Baele, Nuno R Faria, Daniel J Park, Jason T Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah L Caddy, Matthew Cotten, Jonathan D'Ambrozio, Simon Dellicour, Antonino Di Caro, Joseph W Diclaro, Sophie Duraffour, Michael J Elmore, Lawrence S Fakoli, Ousmane Faye, Merle L Gilbert, Sahr M Gevao, Stephen Gire, Adrienne Gladden-Young, Andreas Gnirke, Augustine Goba, Donald S Grant, Bart L Haagmans, Julian A Hiscox, Umaru Jah, Jeffrey R Kugelman, Di Liu, Jia Lu, Christine M Malboeuf, Suzanne Mate, David A Matthews, Christian B Matranga, Luke W Meredith, James Qu, Joshua Quick, Susan D Pas, My V T Phan, Georgios Pollakis, Chantal B Reusken, Mariano Sanchez-Lockhart, Stephen F Schaffner, John S Schieffelin, Rachel S Sealfon, Etienne Simon-Loriere, Saskia L Smits, Kilian Stoecker, Lucy Thorne, Ekaete Alice Tobin, Mohamed A Vandi, Simon J Watson, Kendra West, Shannon Whitmer, Michael R Wiley, Sarah M Winnicki, Shirlee Wohl, Roman Wolfel, Nathan L Yozwiak, Kristian G Andersen, Sylvia O Blyden, Fatorma Bolay, Miles W Carroll, Bernice Dahn, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George F Gao, Robert F Garry, Ian Goodfellow, Stephan Gunther, Christian T Happi, Edward C Holmes, Brima Kargbo, Sakoba Keita, Paul Kellam, Marion P G Koopmans, Jens H Kuhn, Nicholas J Loman, N'faly Magassouba, Dhamari Naidoo, Stuart T Nichol, Tolbert Nyenswah, Gustavo Palacios, Oliver G Pybus, Pardis C Sabeti, Amadou Sall, Ute Stroher, Isatta Wurie, Marc A Suchard, Philippe Lemey, and Andrew Rambaut. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature, April 2017. ISSN 0028-0836, 1476-4687. doi: 10.1038/nature22040. URL http://dx.doi.org/10.1038/nature22040.
J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17:268-276, 1981.
Joseph Felsenstein. *Inferring Phylogenies*. Sinauer associates, 2 edition, 2004.
J. R. Garey, T. J. Near, M. R. Nonnemacher, and S. A. Nadler. Molecular evidence for Acanthocephala as a subtaxon of Rotifera. Mol. Evol., 43:287-292, 1996.
Justin Gilmer, Samuel S. Schoenholz, Patrick F. Riley, Oriol Vinyals, and George E. Dahl. Neural message passing for quantum chemistry. ArXiv, abs/1704.01212, 2017.
S. B. Hedges, K. D. Moberg, and L. R. Maxson. Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and review of the evidence for amniote relationships. Mol. Biol. Evol., 7:607-633, 1990.
D. A. Henk, A. Weir, and M. Blackwell. Laboulbeniopsis termitarius, an ectoparasite of termites newly recognized as a member of the Laboulbeniomycetes. Mycologia, 95:561-564, 2003.
Sebastian Hohn and Alexei J. Drummond. Guided tree topology proposals for Bayesian phylogenetic inference. Syst. Biol., 61(1):1-11, January 2012. ISSN 1063-5157. doi: 10.1093/sysbio/syr074. URL http://dx.doi.org/10.1093/sysbio/syr074.
J. P. Huelsenbeck, F. Ronquist, R. Nielsen, and J. P. Bollback. Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294:2310-2314, 2001.