Clustal

Clustal is a widely used series of computer programs used in bioinformatics for multiple sequence alignment. These programs are primarily used to align nucleotide or protein sequences to identify regions of similarity, which may indicate functional, structural, or evolutionary relationships. The Clustal series includes several versions, such as ClustalW, ClustalX, and Clustal Omega, each offering improvements and refinements in alignment algorithms and user interface.

The core function of Clustal is to take multiple input sequences and, through a progressive alignment method, construct a multiple sequence alignment. This method involves first performing pairwise alignments between all sequences to generate a distance matrix. This matrix is then used to create a guide tree, which approximates the evolutionary relationships between the sequences. The alignment then proceeds by aligning the most closely related sequences first, followed by progressively adding more distant sequences to the alignment, guided by the tree.

Clustal has been instrumental in numerous biological studies, enabling researchers to identify conserved regions in sequences, predict protein structures, infer phylogenetic relationships, and design primers for polymerase chain reaction (PCR). Its accessibility and relative ease of use have made it a popular tool for both novice and experienced bioinformaticians. While newer and more sophisticated alignment algorithms have emerged, Clustal remains a foundational tool in the field due to its historical significance and broad applicability.