When to use Clustal Can be used to align any group of protein or nucleic acid sequences that are related to each other over their entire lengths. Clustal is optimized to align sets of sequences that are entirely colinear, i.e. sequences that have the same protein domains, in the same order. Few Sequences - An alignment of less than 10 distantly related sequences could be unreliable.
Sequences are partially related Sequences include short non overlapping fragments.