/usr/include/Bpp/Seq/Alphabet/ is in libbpp-seq-dev 2.1.0-1.
This file is owned by root:root, with mode 0o755.
..
/usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h
/usr/include/Bpp/Seq/Alphabet/Alphabet.h
/usr/include/Bpp/Seq/Alphabet/AlphabetExceptions.h
/usr/include/Bpp/Seq/Alphabet/AlphabetState.h
/usr/include/Bpp/Seq/Alphabet/AlphabetTools.h
/usr/include/Bpp/Seq/Alphabet/BinaryAlphabet.h
/usr/include/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h
/usr/include/Bpp/Seq/Alphabet/CodonAlphabet.h
/usr/include/Bpp/Seq/Alphabet/DNA.h
/usr/include/Bpp/Seq/Alphabet/DefaultAlphabet.h
/usr/include/Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.h
/usr/include/Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.h
/usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h
/usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h
/usr/include/Bpp/Seq/Alphabet/NucleicAlphabetState.h
/usr/include/Bpp/Seq/Alphabet/ProteicAlphabet.h
/usr/include/Bpp/Seq/Alphabet/ProteicAlphabetState.h
/usr/include/Bpp/Seq/Alphabet/RNA.h
/usr/include/Bpp/Seq/Alphabet/RNY.h
/usr/include/Bpp/Seq/Alphabet/StandardCodonAlphabet.h
/usr/include/Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.h
/usr/include/Bpp/Seq/Alphabet/WordAlphabet.h
/usr/include/Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.h
/usr/include/Bpp/Seq/AlphabetIndex/AAChargeIndex.h
/usr/include/Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h
/usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h
/usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h
/usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h
/usr/include/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h
/usr/include/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h
/usr/include/Bpp/Seq/AlphabetIndex/AAMassIndex.h
/usr/include/Bpp/Seq/AlphabetIndex/AASEA1030Index.h
/usr/include/Bpp/Seq/AlphabetIndex/AASEAInf10Index.h
/usr/include/Bpp/Seq/AlphabetIndex/AASEASup30Index.h
/usr/include/Bpp/Seq/AlphabetIndex/AASurfaceIndex.h
/usr/include/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h
/usr/include/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h
/usr/include/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h
/usr/include/Bpp/Seq/AlphabetIndex/BLOSUM50.h
/usr/include/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h
/usr/include/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h
/usr/include/Bpp/Seq/AlphabetIndex/GranthamAAPolarityIndex.h
/usr/include/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h
/usr/include/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h
/usr/include/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h
/usr/include/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h
/usr/include/Bpp/Seq/AlphabetIndex/SimpleScore.h