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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.
Biorxiv : the Preprint Server for Biology
|March 18, 2026
Summary
We developed CAPHEINE, a computational workflow for pathogen evolutionary analysis using unaligned sequences and a reference genome. This tool aids in studying selection dynamics and evolutionary pressures across different lineages.
Area of Science:
- Computational Biology
- Evolutionary Biology
- Bioinformatics
Background:
- Understanding pathogen evolution is crucial for public health.
- Analyzing evolutionary dynamics requires robust computational tools.
Purpose of the Study:
- To present CAPHEINE, a novel computational workflow.
- To enable comprehensive exploratory evolutionary analysis of pathogen sequences.
Main Methods:
- The workflow accepts unaligned pathogen sequences and a reference genome.
- It performs exploratory evolutionary analysis.
Main Results:
- CAPHEINE facilitates studies on site-level selection dynamics.
- It supports analysis of gene-level positive selection.
- The workflow aids in identifying lineage-specific shifts in selective pressure.
Conclusions:
- CAPHEINE provides a portable and comprehensive solution for pathogen evolutionary analysis.
- It is compatible with Mac OS, Windows, and Linux.
- The workflow is freely available for research use.
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