Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression

Leo A Featherstone; Andrew Rambaut; Sebastian Duchene; Wytamma Wirth

doi:10.1093/sysbio/syae003

Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression

Syst Biol. 2024 Feb 17:syae003. doi: 10.1093/sysbio/syae003. Online ahead of print.

Authors

Leo A Featherstone¹, Andrew Rambaut², Sebastian Duchene³, Wytamma Wirth¹

Affiliations

¹ Peter Doherty Institute for Infection and Immunity, University of Melbourne, Australia.
² Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
³ Department of Computational Biology, Institut Pasteur, Paris, France.

PMID: 38366939
DOI: 10.1093/sysbio/syae003

Abstract

Molecular sequence data from rapidly evolving organisms are often sampled at different points in time. Sampling times can then be used for molecular clock calibration. The root-to-tip (RTT) regression is an essential tool to assess the degree to which the data behave in a clock-like fashion. Here, we introduce Clockor2, a client-side web application for conducting RTT regression. Clockor2 allows users to quickly fit local and global molecular clocks, thus handling the increasing complexity of genomic datasets that sample beyond the assumption of homogeneous host populations. Clockor2 is efficient, handling trees of up to the order of 104 tips, with significant speed increases compared to other RTT regression applications. Although clockor2 is written as a web application, all data processing happens on the client-side, meaning that data never leaves the user's computer. Clockor2 is freely available at https : //clockor2.github.io/.

Keywords: Molecular clock; evolutionary rate heterogeneity; root-to-tip regression.