Table 1.

Description of Data Sets Used to Derive Simulation Parameters.

Name	Type	Length	Mean Site Entropy	Mean Site dN/dS
1B4T_A	Natural	115	1.12	0.27
1W7W_B	Natural	125	0.95	0.23
2CFE_A	Natural	151	0.92	0.21
2BCG_Y	Natural	156	1.01	0.26
1G58_B	Natural	165	1.06	0.25
1GV3_A	Natural	176	1.08	0.26
1V9S_B	Natural	177	1.10	0.27
2FLI_A	Natural	190	1.20	0.30
1RII_A	Natural	195	1.13	0.27
1R6M_A	Natural	203	1.13	0.28
1IBS_A	Natural	291	1.07	0.28
Gal4a	DMS	64	1.92	0.47
LACb	DMS	262	2.08	0.61
NPc	DMS	498	2.38	0.70
HAd	DMS	564	2.25	0.63

Note.—The Type column indicates whether the source of simulation parameters was a natural alignment (“Natural”) or deep-mutational scanning data (“DMS”). Natural alignments are named according to their corresponding PDB [Protein Data Bank (Berman et al. 2000)] ID and chain, i.e., the name 1B4T_A corresponds to PBD ID 1B4T, chain A.

^aYeast Gal4.

^bTEM-1 β-lactamase.

^cInfluenza nucleoprotein.

^dInfluenza H1N1 hemgglutinin.