/usr/include/Bpp/Phyl/Io/ is in libbpp-phyl-dev 2.1.0-1.
This file is owned by root:root, with mode 0o755.
..
/usr/include/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h
/usr/include/Bpp/Phyl/Io/BppORateDistributionFormat.h
/usr/include/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h
/usr/include/Bpp/Phyl/Io/IoDistanceMatrix.h
/usr/include/Bpp/Phyl/Io/IoDistanceMatrixFactory.h
/usr/include/Bpp/Phyl/Io/IoFrequenciesSet.h
/usr/include/Bpp/Phyl/Io/IoFrequenciesSetFactory.h
/usr/include/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h
/usr/include/Bpp/Phyl/Io/IoSubstitutionModel.h
/usr/include/Bpp/Phyl/Io/IoSubstitutionModelFactory.h
/usr/include/Bpp/Phyl/Io/IoTree.h
/usr/include/Bpp/Phyl/Io/IoTreeFactory.h
/usr/include/Bpp/Phyl/Io/Newick.h
/usr/include/Bpp/Phyl/Io/NexusIoTree.h
/usr/include/Bpp/Phyl/Io/Nhx.h
/usr/include/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h