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Genome Biology and Evolution|July 16, 2026
CAPHEINE, or Everything and the Kitchen Sink: A Workflow for Automating Selection Analyses Using HyPhyHannah Verdonk, Danielle Callan, Sergei L Kosakovsky PondGenome Biology and Evolution|July 28, 2026
Beyond Invariable Sites: Using Evolutionary Stasis to Map Multilayered Constraints on the Evolution of Viral and Mammalian GenomesSergei L Kosakovsky Pond, Hannah Verdonk, Steven Weaver, et al.Biorxiv : the Preprint Server for Biology|April 17, 2026
Beyond Invariable Sites: Using Evolutionary Stasis to Map Multi-Layered Constraints on the Evolution of Viral and Mammalian GenomesSergei L Kosakovsky Pond, Hannah Verdonk, Steven Weaver, et al.Biorxiv : the Preprint Server for Biology|March 18, 2026
CAPHEINE, or everything and the kitchen sink: a workflow for automating selection analyses using HyPhyHannah Elaine Verdonk, Danielle Callan, Sergei L Kosakovsky PondJournal of Molecular Evolution|July 11, 2006
Evidence for positive selection on a sexual reproduction gene in the diatom genus Thalassiosira (Bacillariophyta)Ulf Sorhannus, Sergei L Kosakovsky PondSystematic Biology|November 17, 2004
Column sorting: rapid calculation of the phylogenetic likelihood functionSergei L Kosakovsky Pond, Spencer V MusePeerj|February 10, 2018
Relative evolutionary rate inference in HyPhy with LEISRStephanie J Spielman, Sergei L Kosakovsky PondMolecular Biology and Evolution|June 21, 2018
Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution ModelStephanie J Spielman, Sergei L Kosakovsky PondMolecular Biology and Evolution|June 28, 2011
Purifying selection can obscure the ancient age of viral lineagesJoel O Wertheim, Sergei L Kosakovsky PondArxiv|July 1, 2024
AOC: Analysis of Orthologous Collections - an application for the characterization of natural selection in protein-coding sequencesAlexander G Lucaci, Sergei L Kosakovsky PondPageof 21