Genotype-Habitat Association Pipeline

• A computational pipeline that enables cross-species genotype-phenotype association at the tree-of-life scale.
• Written by Menghan Liu, Tavazoie lab @ Columbia University

🔗 Links

• Publication
• Genotype-habitat association

📖 Wiki & Tutorials

For detailed documentation and tutorials, visit the Wiki.

When posting your questions in Issues, please include the full command you used to run gephe.

📜 Citation

If you use this pipeline for your research, please cite:

• Liu M, et al. "Conserved Gene Modules Govern Microbial Colonization of the Mammalian Gut." Cell, 2025.