FUBAR: a fast, unconstrained bayesian approximation for inferring selection von Murrell, Ben, Moola, Sasha, Mabona, Amandla, Weighill, Thomas, Sheward, Daniel, Kosakovsky Pond, Sergei L, Scheffler, Konrad

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Detecting individual sites subject to episodic diversifying selection von Murrell, Ben, Wertheim, Joel O, Moola, Sasha, Weighill, Thomas, Scheffler, Konrad, Kosakovsky Pond, Sergei L

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The biological and clinical significance of emerging SARS-CoV-2 variants von Tao, Kaiming, Tzou, Philip L., Nouhin, Janin, Gupta, Ravindra K., de Oliveira, Tulio, Kosakovsky Pond, Sergei L., Fera, Daniela, Shafer, Robert W.

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Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons von Tzou, Philip L, Tao, Kaiming, Pond, Sergei L Kosakovsky, Shafer, Robert W

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Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection von Smith, Martin D, Wertheim, Joel O, Weaver, Steven, Murrell, Ben, Scheffler, Konrad, Kosakovsky Pond, Sergei L

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Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes von Weaver, Steven, Shank, Stephen D, Spielman, Stephanie J, Li, Michael, Muse, Spencer V, Kosakovsky Pond, Sergei L

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RELAX: detecting relaxed selection in a phylogenetic framework von Wertheim, Joel O, Murrell, Ben, Smith, Martin D, Kosakovsky Pond, Sergei L, Scheffler, Konrad

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Datamonkey: rapid detection of selective pressure on individual sites of codon alignments von Pond, Sergei L. Kosakovsky, Frost, Simon D. W.

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The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages von Martin, Darren P., Weaver, Steven, Tegally, Houriiyah, San, James Emmanuel, Shank, Stephen D., Wilkinson, Eduan, Lucaci, Alexander G., Giandhari, Jennifer, Naidoo, Sureshnee, Pillay, Yeshnee, Singh, Lavanya, Lessells, Richard J., Gupta, Ravindra K., Wertheim, Joel O., Nekturenko, Anton, Murrell, Ben, Harkins, Gordon W., Lemey, Philippe, MacLean, Oscar A., Robertson, David L., de Oliveira, Tulio, Kosakovsky Pond, Sergei L.

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Gene-wide identification of episodic selection von Murrell, Ben, Weaver, Steven, Smith, Martin D, Wertheim, Joel O, Murrell, Sasha, Aylward, Anthony, Eren, Kemal, Pollner, Tristan, Martin, Darren P, Smith, Davey M, Scheffler, Konrad, Kosakovsky Pond, Sergei L

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A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection von Kosakovsky Pond, Sergei L., Murrell, Ben, Fourment, Mathieu, Frost, Simon D.W., Delport, Wayne, Scheffler, Konrad

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HyPhy: hypothesis testing using phylogenies von Pond, Sergei L. Kosakovsky, Frost, Simon D. W., Muse, Spencer V.

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HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens von Kosakovsky Pond, Sergei L, Weaver, Steven, Leigh Brown, Andrew J, Wertheim, Joel O

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Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen von MacLean, Oscar A, Lytras, Spyros, Weaver, Steven, Singer, Joshua B, Boni, Maciej F, Lemey, Philippe, Kosakovsky Pond, Sergei L, Robertson, David L

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Social and Genetic Networks of HIV-1 Transmission in New York City von Wertheim, Joel O, Kosakovsky Pond, Sergei L, Forgione, Lisa A, Mehta, Sanjay R, Murrell, Ben, Shah, Sharmila, Smith, Davey M, Scheffler, Konrad, Torian, Lucia V

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Purifying Selection Can Obscure the Ancient Age of Viral Lineages von Wertheim, Joel O., Kosakovsky Pond, Sergei L.

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HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies von Kosakovsky Pond, Sergei L, Poon, Art F Y, Velazquez, Ryan, Weaver, Steven, Hepler, N Lance, Murrell, Ben, Shank, Stephen D, Magalis, Brittany Rife, Bouvier, Dave, Nekrutenko, Anton, Wisotsky, Sadie, Spielman, Stephanie J, Frost, Simon D W, Muse, Spencer V

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Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage von Farrer, Rhys A, Weinert, Lucy A, Bielby, Jon, Garner, Trenton W. J, Balloux, Francois, Clare, Frances, Bosch, Jaime, Cunningham, Andrew A, Weldon, Che, du Preez, Louis H, Anderson, Lucy, Pond, Sergei L. Kosakovsky, Shahar-Golan, Revital, Henk, Daniel A, Fisher, Matthew C

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Persistent HIV-1 replication maintains the tissue reservoir during therapy von Lorenzo-Redondo, Ramon, Fryer, Helen R., Bedford, Trevor, Kim, Eun-Young, Archer, John, Kosakovsky Pond, Sergei L., Chung, Yoon-Seok, Penugonda, Sudhir, Chipman, Jeffrey G., Fletcher, Courtney V., Schacker, Timothy W., Malim, Michael H., Rambaut, Andrew, Haase, Ashley T., McLean, Angela R., Wolinsky, Steven M.

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POMK mutations disrupt muscle development leading to a spectrum of neuromuscular presentations von Di Costanzo, Stefania, Balasubramanian, Anuradha, Pond, Heather L., Rozkalne, Anete, Pantaleoni, Chiara, Saredi, Simona, Gupta, Vandana A., Sunu, Christine M., Yu, Timothy W., Kang, Peter B., Salih, Mustafa A., Mora, Marina, Gussoni, Emanuela, Walsh, Christopher A., Manzini, M. Chiara

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