This notebook performs pairwise protein structural alignments using the US-align algorithm by Zhang et al. (2022) (an updated version of TM-align by by Zhang and Skolnick (2005)), then constructs a phylogenetic tree using the UPGMA algorithm to visualise similarities.
Designed to run directly in Google Colab for ease-of-use and to remove any local hardware requirements. This implementation also includes multiprocessing support for dramatically increased performance over the base US-align program.
Made possible with US-align and Biopython. Based on mTM-align by Dong et al. (2018).