Not logged in Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models Sianga-Mete, Rita; Hartnady, Penelope; Mandikumba, Wimbai Caroline; Rutherford, Kayleigh; Currin, Christopher Brian; Phelanyane, Florence; Stefan, Sabina; Weaver, Steven; Kosakovsky Pond, Sergei L.; Martin, Darren P. Share Save
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Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa Tegally, Houriiyah; Moir, Monika; Everatt, Josie; Giovanetti, Marta; Scheepers, Cathrine; Wilkinson, Eduan; Subramoney, Kathleen; Makatini, Zinhle; Moyo, Sikhulile; Amoako, Daniel G.; Baxter, Cheryl; Althaus, Christian L.; Anyaneji, Ugochukwu J.; Kekana, Dikeledi; Viana, Raquel; Giandhari, Jennifer; Lessells, Richard J.; Maponga, Tongai; Maruapula, Dorcas; Choga, Wonderful; Matshaba, Mogomotsi; Mbulawa, Mpaphi B.; Msomi, Nokukhanya; Naidoo, Yeshnee; Pillay, Sureshnee; Sanko, Tomasz Janusz; San, James E.; Scott, Lesley; Singh, Lavanya; Magini, Nonkululeko A.; Smith-Lawrence, Pamela; Stevens, Wendy; Dor, Graeme; Tshiabuila, Derek; Wolter, Nicole; Preiser, Wolfgang; Treurnicht, Florette K.; Venter, Marietjie; Chiloane, Georginah; McIntyre, Caitlyn; O'Toole, Aine; Ruis, Christopher; Peacock, Thomas P.; Roemer, Cornelius; Kosakovsky Pond, Sergei L.; Williamson, Carolyn; Pybus, Oliver G.; Bhiman, Jinal N.; Glass, Allison; Martin, Darren P.; Jackson, Ben; Rambaut, Andrew; Laguda-Akingba, Oluwakemi; Gaseitsiwe, Simani; von Gottberg, Anne; de Oliveira, Tulio; Bester, Armand Phillip; Claassen, Mathilda; Doolabh, Deelan; Mudau, Innocent; Mbhele, Nokuzola; Engelbrecht, Susan; Goedhals, Dominique; Hardie, Diana; Hsiao, Nei-Yuan; Iranzadeh, Arash; Ismail, Arshad; Joseph, Rageema; Maharaj, Arisha; Mahlangu, Boitshoko; Mahlakwane, Kamela; Davis, Ashlyn; Marais, Gert; Mlisana, Koleka; Mnguni, Anele; Mohale, Thabo; Motsatsi, Gerald; Mwangi, Peter; Ntuli, Noxolo; Nyaga, Martin; Olubayo, Luicer; Radibe, Botshelo; Ramphal, Yajna; Ramphal, Upasana; Strasheim, Wilhelmina; Tebeila, Naume; van Wyk, Stephanie; Wilson, Shannon; Lucaci, Alexander G.; Weaver, Steven; Maharaj, Akhil; Pillay, Yusasha; Davids, Michaela; Mendes, Adriano; Mayaphi, Simnikiwe Share Save
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function Martin, Darren P.; Lytras, Spyros; Lucaci, Alexander G.; Maier, Wolfgang; Gruening, Bjoern; Shank, Stephen D.; Weaver, Steven; MacLean, Oscar A.; Orton, Richard J.; Lemey, Philippe; Boni, Maciej F.; Tegally, Houriiyah; Harkins, Gordon W.; Scheepers, Cathrine; Bhiman, Jinal N.; Everatt, Josie; Amoako, Daniel G.; San, James Emmanuel; Giandhari, Jennifer; Sigal, Alex; Williamson, Carolyn; Hsiao, Nei-yuan; von Gottberg, Anne; De Klerk, Arne; Shafer, Robert W.; Robertson, David L.; Wilkinson, Robert J.; Sewell, B. Trevor; Lessells, Richard; Nekrutenko, Anton; Greaney, Allison J.; Starr, Tyler N.; Bloom, Jesse D.; Murrell, Ben; Wilkinson, Eduan; Gupta, Ravindra K.; de Oliveira, Tulio; Kosakovsky Pond, Sergei L. Share Save
Predicting the mutational drivers of future SARS-CoV-2 variants of concern Maher, M. Cyrus; Bartha, Istvan; Weaver, Steven; di Iulio, Julia; Ferri, Elena; Soriaga, Leah; Lempp, Florian A.; Hie, Brian L.; Bryson, Bryan; Berger, Bonnie; Robertson, David L.; Snell, Gyorgy; Corti, Davide; Virgin, Herbert W.; Pond, Sergei L. Kosakovsky; Telenti, Amalio Share Save
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HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies Pond, Sergei L. Kosakovsky; 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 Share Save
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Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples Smith, Melissa Laird; Murrell, Ben; Eren, Kemal; Ignacio, Caroline; Landais, Elise; Weaver, Steven; Pham Phung; Ludka, Colleen; Hepler, Lance; Caballero, Gemma; Pollner, Tristan; Guo, Yan; Richman, Douglas; Poignard, Pascal; Paxinos, Ellen E.; Pond, Sergei L. Kosakovsky; Smith, Davey M. Share Save
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Gene-Wide Identification of Episodic Selection 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; Pond, Sergei L. Kosakovsky Share Save
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