Bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression.

ABSTRACT: The composition of the latent human immunodeficiency virus 1 (HIV-1) reservoir is shaped by when proviruses integrated into host genomes. These integration dates can be estimated by phylogenetic methods like root-to-tip (RTT) regression. However, RTT does not accommodate variation in the number of mutations over time, uncertainty in estimating the molecular clock, or the position of the root in the tree. To address these limitations, we implemented a Bayesian extension of RTT as an R package (bayroot), which enables the user to incorporate prior information about the time of infection and start of antiretroviral therapy. Taking an unrooted maximum likelihood tree as input, we use a Metropolis-Hastings algorithm to sample from the joint posterior distribution of three parameters (the

SUBMITTER: Ferreira RC 

PROVIDER: S-EPMC9825830 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature