CAPHEINE, or Everything and the Kitchen Sink: A Workflow for Automating Selection Analyses Using HyPhy

Area of Science:

• Computational Biology
• Evolutionary Biology
• Bioinformatics

Background:

• Understanding pathogen evolution is crucial for public health.
• Analyzing pathogen genomic data reveals insights into selection pressures and evolutionary trajectories.

Purpose of the Study:

• To present CAPHEINE, a novel computational workflow for comprehensive evolutionary analysis of pathogen sequences.
• To provide researchers with a portable and user-friendly tool for exploring evolutionary dynamics.

Main Methods:

• CAPHEINE accepts unaligned pathogen sequences and a reference genome.
• The workflow performs exploratory evolutionary analysis, including site-level and gene-level selection dynamics.
• It is designed for portability across Mac OS, Windows, and Linux.

Main Results:

• CAPHEINE facilitates detailed studies of selection dynamics.
• The workflow supports the investigation of positive selection and lineage-specific shifts in selective pressure.
• It enables researchers to focus on interpreting evolutionary results.

Conclusions:

• CAPHEINE offers a robust solution for pathogen evolutionary analysis.
• The workflow enhances the study of molecular evolution and pathogen adaptation.
• Freely available at https://github.com/veg/CAPHEINE, CAPHEINE empowers researchers with advanced analytical capabilities.