ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models von Darriba, Diego, Posada, David, Kozlov, Alexey M, Stamatakis, Alexandros, Morel, Benoit, Flouri, Tomas

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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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Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations von Duchene, Sebastian, Lemey, Philippe, Stadler, Tanja, Ho, Simon Y W, Duchene, David A, Dhanasekaran, Vijaykrishna, Baele, Guy

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Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function von Martin, Darren P., Lytras, Spyros, Lucaci, Alexander G., Maier, Wolfgang, Grüning, Björn, 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.

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Beginner's Guide on the Use of PAML to Detect Positive Selection von Álvarez-Carretero, Sandra, Kapli, Paschalia, Yang, Ziheng

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Phylogenomic Resolution of Sea Spider Diversification through Integration of Multiple Data Classes von Ballesteros, Jesús A, Setton, Emily V W, Santibáñez-López, Carlos E, Arango, Claudia P, Brenneis, Georg, Brix, Saskia, Corbett, Kevin F, Cano-Sánchez, Esperanza, Dandouch, Merai, Dilly, Geoffrey F, Eleaume, Marc P, Gainett, Guilherme, Gallut, Cyril, McAtee, Sean, McIntyre, Lauren, Moran, Amy L, Moran, Randy, López-González, Pablo J, Scholtz, Gerhard, Williamson, Clay, Woods, H Arthur, Zehms, Jakob T, Wheeler, Ward C, Sharma, Prashant P

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Fundamental Identifiability Limits in Molecular Epidemiology von Louca, Stilianos, McLaughlin, Angela, MacPherson, Ailene, Joy, Jeffrey B, Pennell, Matthew W

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AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era von Ly-Trong, Nhan, Naser-Khdour, Suha, Lanfear, Robert, Minh, Bui Quang

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Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril von Wisotsky, Sadie R, Kosakovsky Pond, Sergei L, Shank, Stephen D, Muse, Spencer V

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Contrast-FEL—A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches von Kosakovsky Pond, Sergei L, Wisotsky, Sadie R, Escalante, Ananias, Magalis, Brittany Rife, Weaver, Steven

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HAlign 3: Fast Multiple Alignment of Ultra-Large Numbers of Similar DNA/RNA Sequences von Tang, Furong, Chao, Jiannan, Wei, Yanming, Yang, Fenglong, Zhai, Yixiao, Xu, Lei, Zou, Quan

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Global Patterns of Recombination across Human Viruses von Patiño-Galindo, Juan Ángel, Filip, Ioan, Rabadan, Raul

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Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies von Didelot, Xavier, Siveroni, Igor, Volz, Erik M

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Evolutionary Processes in the Emergence and Recent Spread of the Syphilis Agent, Treponema pallidum von Pla-Díaz, Marta, Sánchez-Busó, Leonor, Giacani, Lorenzo, Šmajs, David, Bosshard, Philipp P, Bagheri, Homayoun C, Schuenemann, Verena J, Nieselt, Kay, Arora, Natasha, González-Candelas, Fernando

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Genomic Evidence for Speciation with Gene Flow in Broadcast Spawning Marine Invertebrates von Hirase, Shotaro, Yamasaki, Yo Y, Sekino, Masashi, Nishisako, Masato, Ikeda, Minoru, Hara, Motoyuki, Merilä, Juha, Kikuchi, Kiyoshi

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Diversity and Evolution of Frog Visual Opsins: Spectral Tuning and Adaptation to Distinct Light Environments von Schott, Ryan K, Fujita, Matthew K, Streicher, Jeffrey W, Gower, David J, Thomas, Kate N, Loew, Ellis R, Bamba Kaya, Abraham G, Bittencourt-Silva, Gabriela B, Guillherme Becker, C, Cisneros-Heredia, Diego, Clulow, Simon, Davila, Mateo, Firneno, Thomas J, Haddad, Célio F B, Janssenswillen, Sunita, Labisko, Jim, Maddock, Simon T, Mahony, Michael, Martins, Renato A, Michaels, Christopher J, Mitchell, Nicola J, Portik, Daniel M, Prates, Ivan, Roelants, Kim, Roelke, Corey, Tobi, Elie, Woolfolk, Maya, Bell, Rayna C

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Jointly Inferring the Dynamics of Population Size and Sampling Intensity from Molecular Sequences von Parag, Kris V, du Plessis, Louis, Pybus, Oliver G

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Forensic genetics and genomics: Much more than just a human affair von Arenas, Miguel, Pereira, Filipe, Oliveira, Manuela, Pinto, Nadia, Lopes, Alexandra M, Gomes, Veronica, Carracedo, Angel, Amorim, Antonio

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Evolutionary history of assassin bugs (insecta: hemiptera: Reduviidae): insights from divergence dating and ancestral state reconstruction von Hwang, Wei Song, Weirauch, Christiane

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Adaptive Radiation of the Flukes of the Family Fasciolidae Inferred from Genome-Wide Comparisons of Key Species von Choi, Young-Jun, Fontenla, Santiago, Fischer, Peter U, Le, Thanh Hoa, Costábile, Alicia, Blair, David, Brindley, Paul J, Tort, Jose F, Cabada, Miguel M, Mitreva, Makedonka

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