@article{mannino_wisotsky_pond_muse_2020, title={Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability}, volume={15}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0229493}, abstractNote={It is standard practice to model site-to-site variability of substitution rates by discretizing a continuous distribution into a small number, K, of equiprobable rate categories. We demonstrate that the variance of this discretized distribution has an upper bound determined solely by the choice of K and the mean of the distribution. This bound can introduce biases into statistical inference, especially when estimating parameters governing site-to-site variability of substitution rates. Applications to two large collections of sequence alignments demonstrate that this upper bound is often reached in analyses of real data. When parameter estimation is of primary interest, additional rate categories or more flexible modeling methods should be considered.}, number={3}, journal={PLOS ONE}, author={Mannino, Frank and Wisotsky, Sadie and Pond, Sergei L. Kosakovsky and Muse, Spencer V}, year={2020}, month={Mar} }
 @article{pond_poon_velazquez_weaver_hepler_murrell_shank_magalis_bouvier_nekrutenko_et al._2020, title={HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies}, volume={37}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msz197}, abstractNote={Abstract}, number={1}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Pond, Sergei L. Kosakovsky and Poon, Art F. Y. and Velazquez, Ryan and Weaver, Steven and Hepler, N. Lance and Murrell, Ben and Shank, Stephen D. and Magalis, Brittany Rife and Bouvier, Dave and Nekrutenko, Anton and et al.}, year={2020}, month={Jan}, pages={295–299} }
 @article{wisotsky_pond_shank_muse_2020, title={Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril}, volume={37}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msaa037}, abstractNote={Abstract}, number={8}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Wisotsky, Sadie R. and Pond, Sergei L. Kosakovsky and Shank, Stephen D. and Muse, Spencer V}, year={2020}, month={Aug}, pages={2430–2439} }