/usr/include/Bpp/Phyl/Model/Nucleotide/ is in libbpp-phyl-dev 2.1.0-1ubuntu3.
This file is owned by root:root, with mode 0o755.
..
/usr/include/Bpp/Phyl/Model/Nucleotide/F84.h
/usr/include/Bpp/Phyl/Model/Nucleotide/GTR.h
/usr/include/Bpp/Phyl/Model/Nucleotide/HKY85.h
/usr/include/Bpp/Phyl/Model/Nucleotide/JCnuc.h
/usr/include/Bpp/Phyl/Model/Nucleotide/K80.h
/usr/include/Bpp/Phyl/Model/Nucleotide/L95.h
/usr/include/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Nucleotide/RN95.h
/usr/include/Bpp/Phyl/Model/Nucleotide/RN95s.h
/usr/include/Bpp/Phyl/Model/Nucleotide/SSR.h
/usr/include/Bpp/Phyl/Model/Nucleotide/T92.h
/usr/include/Bpp/Phyl/Model/Nucleotide/TN93.h
/usr/include/Bpp/Phyl/Model/Nucleotide/YpR.h
/usr/include/Bpp/Phyl/Model/Nucleotide/gBGC.h