/usr/share/hyphy/SubstitutionClasses/ is in hyphy-common 2.2.7+dfsg-1.
This file is owned by root:root, with mode 0o755.
..
/usr/share/hyphy/SubstitutionClasses/AAEFV/
/usr/share/hyphy/SubstitutionClasses/AAEFV/Equal
/usr/share/hyphy/SubstitutionClasses/AAEFV/Estimated
/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set
/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Partition
/usr/share/hyphy/SubstitutionClasses/CodonEFV/
/usr/share/hyphy/SubstitutionClasses/CodonEFV/Equal
/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Codon
/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params.
/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params.
/usr/share/hyphy/SubstitutionClasses/Heterogeneity/
/usr/share/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete
/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta
/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma
/usr/share/hyphy/SubstitutionClasses/Heterogeneity/General Discrete
/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Half Normal
/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Lognormal
/usr/share/hyphy/SubstitutionClasses/NucEFV/
/usr/share/hyphy/SubstitutionClasses/NucEFV/Equal
/usr/share/hyphy/SubstitutionClasses/NucEFV/Estimated
/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set
/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Partition
/usr/share/hyphy/SubstitutionClasses/aa.bf
/usr/share/hyphy/SubstitutionClasses/codon.bf
/usr/share/hyphy/SubstitutionClasses/dinuc.bf
/usr/share/hyphy/SubstitutionClasses/nuc.bf