Table 1. Influenza A virus mutations identified as significantly beneficial by MMC-ABC.

	Segment	Position	Substitution type	Initial freq. (%)	Final freq. (%)	WF-ABC s estimates (99$\%$ HPDIs)	MMC-ABC s estimates (99$\%$ HPDIs)
Control 1	HA	1395	Nonsynonymous	$0.03$	$92.5$	0.12 (0.05, 0.19)	0.14 (0.06, 0.21)
Control 2	HA	1211	Nonsynonymous	$0.04$	$100.0$	0.20 (0.08, 0.35)	0.23 (0.15, 0.32)
Drug 1	PA	2194	Synonymous	$1.4$	$36.7$	0.09 (0.02, 0.17)	0.11 (0.05, 0.18)
	HA	48	Synonymous	$0.1$	$92.3$	0.14 (0.06, 0.27)	0.16 (0.05, 0.24)
	HA	1395	Nonsynonymous	$0.06$	$99.9$	0.22 (0.08, 0.34)	0.27 (0.13, 0.42)
	NA	582	Synonymous	$0.02$	$98.3$	0.29 (0.15, 0.45)	0.43 (0.28, 0.56)
	NA	823a	Nonsynonymous	$0.04$	$99.5$	0.15 (0.06, 0.24)	0.18 (0.08, 0.28)
Drug 2	NA	823a	Nonsynonymous	$0.04$	$90.3$	0.27 (0.12, 0.48)	0.26 (0.13, 0.42)

^aSites of known drug-resistance mutations