Over evolutionary time, related DNA or amino acid sequences diverge through the accumulation of mutation events such as nucleotide or amino acid substitutions, insertions and deletions.
A sequence alignment is an attempt to determine regions of homology in a set of sequences. It consists of a table with one sequence per row, and with each column containing homologous residues from the diﬀerent sequences, e.g. residues that are thought to have evolved from a common ancestral nucleotide/amino acid. If it is thought that the ancestral nucleotide/amino acid got lost on the evolutionary path to one descendant sequence, this sequence will show a special gap character “–” in that alignment column.