Dayhoff matrices.

Dayhoff et al. [6] presented a method for estimating the matrix M from the observation of 1572 accepted mutations between 34 superfamilies of closely related sequences. Their method was pioneering in the field. Nowadays we are able to estimate M by more accurate and better founded methods [8,4].

A Dayhoff matrix (in honour of Margaret O. Dayhoff) is a matrix, computed from a 250-PAM mutation matrix, used for the standard dynamic programming method of sequence alignment. The Dayhoff matrix entries are related to M²⁵⁰ by

$$D_{ij} = 10 \log_{10} \frac{(M^{250})_{ij}}{f_i}$$