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bioRxiv · 10.64898/2026.02.23.707482

CAPHEINE, or everything and the kitchen sink: a workflow for automating selection analyses using HyPhy

Verdonk, H. E.·Callan, D.·Kosakovsky Pond, S. L.
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Abstract

SummaryHere we present CAPHEINE, a computational workflow that starts with a set of unaligned pathogen sequences and a reference genome and performs a comprehensive exploratory evolutionary analysis of the input data. CAPHEINE pairs nicely with studies of site-level selection dynamics, gene-level positive selection, and lineage-specific shifts in selective pressure. Our workflow is portable across Mac OS, Windows, and Linux, allowing researchers to focus on results. Availability and ImplementationCAPHEINE is freely available at https://github.com/veg/CAPHEINE, along with a set of usage instructions.

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Verdonk, H. E., Callan, D., Kosakovsky Pond, S. L.. 2026-02-24. CAPHEINE, or everything and the kitchen sink: a workflow for automating selection analyses using HyPhy. https://doi.org/10.64898/2026.02.23.707482

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