Genome Biology and EvolutionBioinformaticsPeer-reviewed journal article
CAPHEINE, or everything and the kitchen sink: a workflow for automating selection analyses using HyPhy
Hannah VerdonkiD, Danielle CallaniD, Sergei L. Kosakovsky PondiD
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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