Wavess: An R package for simulation of adaptive within-host virus sequence evolution.

ABSTRACT: Simulating within-host virus sequence evolution allows for the investigation of factors such as the role of recombination in virus diversification and the impact of selective pressures on virus evolution. Here, we provide a new software to simulate virus within-host evolution called wavess (within-host adaptive virus evolution sequence simulator), a discrete-time individual-based model and a corresponding user-friendly R package. The underlying model simulates recombination, a latent infected cell reservoir, and three forms of selection: conserved sites fitness and replicative fitness in comparison to a reference sequence, and immune fitness including cross-reactivity imposed by a co-evolving immune response. In the R package, we also provide functions to generate model inputs from empiric

SUBMITTER: Sambaturu N 

PROVIDER: S-EPMC12459828 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature