CAPHEINE, or everything and the kitchen sink: a workflow for automating selection analyses using HyPhy
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ID: 321516
2026
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Abstract
Here 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.
| Reference Key |
openalex_W7169610401
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|---|---|
| Authors | Hannah Verdonk, Danielle Callan, Sergei L Kosakovsky Pond |
| Journal | genome biology and evolution |
| Year | 2026 |
| DOI |
10.1093/gbe/evag173
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| URL | |
| Keywords | Keywords not found |
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