PhytClust is a dynamic-programming-based algorithm for optimal phylogenetic tree clustering. It uses the clustering validity index with prominence-based peak detection to find the best number of clusters.

Please cite this repository if you use the algorithm in your work:
K. Ganesan, E. Billard, T.L. Kaufmann, C. B Strange, M. C. Cwikla, A. Altenhoff, C. Dessimoz, R.F. Schwarz, PhytClust (2025).
https://github.com/schwarzlab-ccb/PhytClust

---

Acknowledgements: C. Robens, L. Godfrey, T. L. Kaufmann.