Table 1. Estimated expected number of mutations per position ${\mu }_{*}$ and estimated fraction of homoplasies for five different subsets of core alignment columns: all columns, all synonymous positions (third positions in fourfold degenerate codons), second positions in codons, synonymous positions excluding the outgroup, and second positions in codons excluding the outgroup.

Column set	${\mu }_{*}$	fh
All columns	0.118	0.026
Synonymous positions	0.287	0.063
Second positions in codons	0.0258	0.006
Synom. pos. without outgroup	0.149	0.033
Sec. pos. without outgroup	0.0172	0.004