/usr/include/Bpp/Phyl/Likelihood/ is in libbpp-phyl-dev 2.1.0-1ubuntu3.
This file is owned by root:root, with mode 0o755.
..
/usr/include/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h
/usr/include/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h
/usr/include/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h
/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h
/usr/include/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h
/usr/include/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h
/usr/include/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h
/usr/include/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h
/usr/include/Bpp/Phyl/Likelihood/RASTools.h
/usr/include/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/SitePartitionTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/TreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodData.h
/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h