On the validity of evolutionary models with site-specific parameters. by Konrad Scheffler, Ben Murrell, Sergei L Kosakovsky Pond

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Benchmarking multi-rate codon models. by Wayne Delport, Konrad Scheffler, Mike B Gravenor, Spencer V Muse, Sergei Kosakovsky Pond

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

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CodonTest: modeling amino acid substitution preferences in coding sequences. by Wayne Delport, Konrad Scheffler, Gordon Botha, Mike B Gravenor, Spencer V Muse, Sergei L Kosakovsky Pond

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Modeling HIV-1 drug resistance as episodic directional selection. by Ben Murrell, Tulio de Oliveira, Chris Seebregts, Sergei L Kosakovsky Pond, Konrad Scheffler, Southern African Treatment and Resistance Network-SATuRN Consortium

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Comparative Analysis of Cell-Associated HIV DNA Levels in Cerebrospinal Fluid and Peripheral Blood by Droplet Digital PCR. by Michelli Faria de Oliveira, Sara Gianella, Scott Letendre, Konrad Scheffler, Sergei L Kosakovsky Pond, Davey M Smith, Matt Strain, Ronald J Ellis

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IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform. by N Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D Richman, Dennis R Burton, Pascal Poignard, Davey M Smith, Sergei L Kosakovsky Pond

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

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REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats by Egor Dolzhenko, Ben Weisburd, Kristina Ibañez, Indhu-Shree Rajan-Babu, Christine Anyansi, Mark F. Bennett, Kimberley Billingsley, Ashley Carroll, Samuel Clamons, Matt C. Danzi, Viraj Deshpande, Jinhui Ding, Sarah Fazal, Andreas Halman, Bharati Jadhav, Yunjiang Qiu, Phillip A. Richmond, Christopher T. Saunders, Konrad Scheffler, Joke J. F. A. van Vugt, Ramona R. A. J. Zwamborn, Genomics England Research Consortium, Samuel S. Chong, Jan M. Friedman, Arianna Tucci, Heidi L. Rehm, Michael A. Eberle

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Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial. by Paul T Edlefsen, Morgane Rolland, Tomer Hertz, Sodsai Tovanabutra, Andrew J Gartland, Allan C deCamp, Craig A Magaret, Hasan Ahmed, Raphael Gottardo, Michal Juraska, Connor McCoy, Brendan B Larsen, Eric Sanders-Buell, Chris Carrico, Sergey Menis, Gustavo H Kijak, Meera Bose, RV144 Sequencing Team, Miguel A Arroyo, Robert J O'Connell, Sorachai Nitayaphan, Punnee Pitisuttithum, Jaranit Kaewkungwal, Supachai Rerks-Ngarm, Merlin L Robb, Tatsiana Kirys, Ivelin S Georgiev, Peter D Kwong, Konrad Scheffler, Sergei L Kosakovsky Pond, Jonathan M Carlson, Nelson L Michael, William R Schief, James I Mullins, Jerome H Kim, Peter B Gilbert

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