/usr/share/hyphy/SubstitutionModels/ is in hyphy-common 2.2.7+dfsg-1.
This file is owned by root:root, with mode 0o755.
..
/usr/share/hyphy/SubstitutionModels/Aminoacid/
/usr/share/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl
/usr/share/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl
/usr/share/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl
/usr/share/hyphy/SubstitutionModels/Aminoacid/Jones.mdl
/usr/share/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl
/usr/share/hyphy/SubstitutionModels/Binary/
/usr/share/hyphy/SubstitutionModels/Binary/F81.mdl
/usr/share/hyphy/SubstitutionModels/Codon/
/usr/share/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl
/usr/share/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl
/usr/share/hyphy/SubstitutionModels/Codon/MG94.mdl
/usr/share/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl
/usr/share/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl
/usr/share/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl
/usr/share/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl
/usr/share/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl
/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl
/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl
/usr/share/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl
/usr/share/hyphy/SubstitutionModels/Nucleotide/
/usr/share/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf
/usr/share/hyphy/SubstitutionModels/Nucleotide/F81.mdl
/usr/share/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl
/usr/share/hyphy/SubstitutionModels/Nucleotide/REV.mdl
/usr/share/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl
/usr/share/hyphy/SubstitutionModels/Nucleotide/TrN.mdl
/usr/share/hyphy/SubstitutionModels/User/
/usr/share/hyphy/SubstitutionModels/User/Nucleotide/
/usr/share/hyphy/SubstitutionModels/User/Nucleotide/JC69
/usr/share/hyphy/SubstitutionModels/User/Nucleotide/K2P