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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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. CAPHEINE is freely available at https://github.com/veg/CAPHEINE, along with a set of usage instructions.
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