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CAPHEINE, or everything and the kitchen sink: a workflow for automating selection analyses using HyPhy
Hannah Elaine Verdonk1, Danielle Callan1, Sergei L Kosakovsky Pond1
1Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, Pennsylvania, USA.
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.
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