HyPhy: The Open-Source Engine Powering Evolutionary Hypothesis Testing
In the era of high-throughput sequencing and precision bioinformatics, understanding how genes evolve across species and conditions is more crucial than ever. HyPhy—short for Hypothesis Testing Using Phylogenies—has emerged as one of the most robust platforms for exploring the forces shaping genetic variation.
Whether you’re studying viral mutations, adaptive evolution, or host-pathogen dynamics, HyPhy provides the analytical horsepower to get meaningful, statistically sound insights.
🌱 What Is HyPhy Used For?
HyPhy is a scientific software package designed for molecular evolution, phylogenetic inference, and genetic sequence analysis. Unlike traditional tree-building tools, HyPhy focuses on how evolution acts at the sequence level—through natural selection, mutation, and recombination.
Core Applications:
- Detecting positive and purifying selection at the codon level
- Modeling site- or branch-specific evolutionary pressure
- Identifying recombination hotspots in aligned sequences
- Performing likelihood-based comparative analyses
- Analyzing ultra-deep sequencing datasets (e.g., viral genomes)
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