Clustal

Clustal is a family of widely used bioinformatics tools for multiple sequence alignment based on the progressive alignment strategy. The original Clustal program, developed by Des Higgins in 1988, was followed by ClustalW and ClustalOmega, each improving speed and accuracy through better guide tree construction and alignment scoring. ClustalOmega introduced hidden Markov model-based profile alignment to handle larger datasets. Despite its popularity, Clustal remains a heuristic, and its accuracy on benchmark datasets has been surpassed by MAFFT and MUSCLE for many sequence types. Clustal remains the default alignment tool in many molecular biology laboratories worldwide.

Clustal's dominance in bioinformatics is a case study in path dependence: it became the standard because it was first, not because it is best.