Datamonkey 3: browser-native molecular evolution analysis.

Abstract

We present Datamonkey 3, a browser-native implementation of the Datamonkey web platform for molecular evolutionary analysis. By utilizing WebAssembly to execute the HyPhy analysis engine on the client side, Datamonkey 3 removes the dependency on remote computational clusters for standard analyses. This architecture ensures data sovereignty by processing sequences locally and enables an interactive workflow with immediate feedback. The platform provides a comprehensive suite of statistical methods for detecting natural selection and recombination, supported by a data curation system that identifies and corrects common formatting errors. Additionally, Datamonkey 3 incorporates data-driven runtime estimation and interactive results visualization. By shifting the computational burden to the client, Datamonkey 3 establishes a sustainable, privacy-preserving infrastructure model that scales with the user base, demonstrating the viability of client-side genomic inference. While tailored for evolutionary analysis of selection and recombination, this browser-native architecture offers a generalizable blueprint for deploying complex bioinformatic tools without server-side dependencies. Datamonkey 3 is freely available at https://v3.datamonkey.org, and all source code is available from https://github.com/veg/datamonkey3.