drwxr-xr-x	root/root	etc/
drwxr-xr-x	root/root	etc/revdep.d/
-rw-r--r--	root/root	etc/revdep.d/bpp1-phyl
drwxr-xr-x	root/root	usr/
drwxr-xr-x	root/root	usr/include/
drwxr-xr-x	root/root	usr/include/Phyl/
-rw-r--r--	root/root	usr/include/Phyl/AbstractAgglomerativeDistanceMethod.h
-rw-r--r--	root/root	usr/include/Phyl/AbstractCodonFrequenciesReversibleSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/AbstractCodonReversibleSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/AbstractDendrogramPlot.h
-rw-r--r--	root/root	usr/include/Phyl/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/AbstractHomogeneousTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/AbstractNonHomogeneousTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/AbstractSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/AbstractTreeDrawing.h
-rw-r--r--	root/root	usr/include/Phyl/AbstractTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/AbstractTreeLikelihoodData.h
-rw-r--r--	root/root	usr/include/Phyl/AbstractTreeParsimonyData.h
-rw-r--r--	root/root	usr/include/Phyl/AbstractTreeParsimonyScore.h
-rw-r--r--	root/root	usr/include/Phyl/AbstractWordReversibleSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/AgglomerativeDistanceMethod.h
-rw-r--r--	root/root	usr/include/Phyl/AnalyticalSubstitutionCount.h
-rw-r--r--	root/root	usr/include/Phyl/AncestralStateReconstruction.h
-rw-r--r--	root/root	usr/include/Phyl/BioNJ.h
-rw-r--r--	root/root	usr/include/Phyl/BipartitionList.h
-rw-r--r--	root/root	usr/include/Phyl/BipartitionTools.h
-rw-r--r--	root/root	usr/include/Phyl/CladogramPlot.h
-rw-r--r--	root/root	usr/include/Phyl/ClockTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/CodonAsynonymousFrequenciesReversibleSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/CodonAsynonymousReversibleSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/CodonNeutralFrequenciesReversibleSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/CodonNeutralReversibleSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/DRASDRTreeLikelihoodData.h
-rw-r--r--	root/root	usr/include/Phyl/DRASRTreeLikelihoodData.h
-rw-r--r--	root/root	usr/include/Phyl/DRHomogeneousMixedTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/DRHomogeneousTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/DRNonHomogeneousMixedTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/DRNonHomogeneousTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/DRTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/DRTreeLikelihoodTools.h
-rw-r--r--	root/root	usr/include/Phyl/DRTreeParsimonyData.h
-rw-r--r--	root/root	usr/include/Phyl/DRTreeParsimonyScore.h
-rw-r--r--	root/root	usr/include/Phyl/DSO78.h
-rw-r--r--	root/root	usr/include/Phyl/DetailedSiteSimulator.h
-rw-r--r--	root/root	usr/include/Phyl/DiscreteRatesAcrossSitesTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/DistanceEstimation.h
-rw-r--r--	root/root	usr/include/Phyl/F84.h
-rw-r--r--	root/root	usr/include/Phyl/FrequenciesSet.h
-rw-r--r--	root/root	usr/include/Phyl/G2001.h
-rw-r--r--	root/root	usr/include/Phyl/GTR.h
-rw-r--r--	root/root	usr/include/Phyl/GY94.h
-rw-r--r--	root/root	usr/include/Phyl/HKY85.h
-rw-r--r--	root/root	usr/include/Phyl/HomogeneousSequenceSimulator.h
-rw-r--r--	root/root	usr/include/Phyl/HomogeneousTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/IODistanceMatrix.h
-rw-r--r--	root/root	usr/include/Phyl/IODistanceMatrixFactory.h
-rw-r--r--	root/root	usr/include/Phyl/IOTree.h
-rw-r--r--	root/root	usr/include/Phyl/IOTreeFactory.h
-rw-r--r--	root/root	usr/include/Phyl/IndexToCount.h
-rw-r--r--	root/root	usr/include/Phyl/JCnuc.h
-rw-r--r--	root/root	usr/include/Phyl/JCprot.h
-rw-r--r--	root/root	usr/include/Phyl/JTT92.h
-rw-r--r--	root/root	usr/include/Phyl/K80.h
-rw-r--r--	root/root	usr/include/Phyl/L95.h
-rw-r--r--	root/root	usr/include/Phyl/MG94.h
-rw-r--r--	root/root	usr/include/Phyl/MarginalAncestralStateReconstruction.h
-rw-r--r--	root/root	usr/include/Phyl/MarkovModulatedSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/MixedSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/MutationProcess.h
-rw-r--r--	root/root	usr/include/Phyl/NNIHomogeneousTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/NNISearchable.h
-rw-r--r--	root/root	usr/include/Phyl/NNITopologySearch.h
-rw-r--r--	root/root	usr/include/Phyl/NeighborJoining.h
-rw-r--r--	root/root	usr/include/Phyl/Newick.h
-rw-r--r--	root/root	usr/include/Phyl/NexusIOTree.h
-rw-r--r--	root/root	usr/include/Phyl/Node.h
-rw-r--r--	root/root	usr/include/Phyl/NodeTemplate.h
-rw-r--r--	root/root	usr/include/Phyl/NonHomogeneousSequenceSimulator.h
-rw-r--r--	root/root	usr/include/Phyl/NonHomogeneousTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/NucleotideSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/OneJumpSubstitutionCount.h
-rw-r--r--	root/root	usr/include/Phyl/OptimizationTools.h
-rw-r--r--	root/root	usr/include/Phyl/PGMA.h
-rw-r--r--	root/root	usr/include/Phyl/PatternTools.h
-rw-r--r--	root/root	usr/include/Phyl/PhylipDistanceMatrixFormat.h
-rw-r--r--	root/root	usr/include/Phyl/PhyloStatistics.h
-rw-r--r--	root/root	usr/include/Phyl/PhylogeneticsApplicationTools.h
-rw-r--r--	root/root	usr/include/Phyl/PhylogramPlot.h
-rw-r--r--	root/root	usr/include/Phyl/ProbabilisticSubstitutionMapping.h
-rw-r--r--	root/root	usr/include/Phyl/ProteinSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/PseudoNewtonOptimizer.h
-rw-r--r--	root/root	usr/include/Phyl/RASTools.h
-rw-r--r--	root/root	usr/include/Phyl/RE08.h
-rw-r--r--	root/root	usr/include/Phyl/RHomogeneousClockTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/RHomogeneousMixedTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/RHomogeneousTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/RNonHomogeneousMixedTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/RNonHomogeneousTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/RateDistributionFactory.h
-rw-r--r--	root/root	usr/include/Phyl/SequenceSimulationTools.h
-rw-r--r--	root/root	usr/include/Phyl/SequenceSimulator.h
-rw-r--r--	root/root	usr/include/Phyl/SimpleSubstitutionCount.h
-rw-r--r--	root/root	usr/include/Phyl/SitePartitionTreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/SitePatterns.h
-rw-r--r--	root/root	usr/include/Phyl/SiteSimulator.h
-rw-r--r--	root/root	usr/include/Phyl/SubstitutionCount.h
-rw-r--r--	root/root	usr/include/Phyl/SubstitutionMapping.h
-rw-r--r--	root/root	usr/include/Phyl/SubstitutionMappingTools.h
-rw-r--r--	root/root	usr/include/Phyl/SubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/SubstitutionModelFactory.h
-rw-r--r--	root/root	usr/include/Phyl/SubstitutionModelSet.h
-rw-r--r--	root/root	usr/include/Phyl/SubstitutionModelSetTools.h
-rw-r--r--	root/root	usr/include/Phyl/T92.h
-rw-r--r--	root/root	usr/include/Phyl/TN93.h
-rw-r--r--	root/root	usr/include/Phyl/TS98.h
-rw-r--r--	root/root	usr/include/Phyl/TopologySearch.h
-rw-r--r--	root/root	usr/include/Phyl/Tree.h
-rw-r--r--	root/root	usr/include/Phyl/TreeDrawing.h
-rw-r--r--	root/root	usr/include/Phyl/TreeExceptions.h
-rw-r--r--	root/root	usr/include/Phyl/TreeLikelihood.h
-rw-r--r--	root/root	usr/include/Phyl/TreeLikelihoodData.h
-rw-r--r--	root/root	usr/include/Phyl/TreeLikelihoodTools.h
-rw-r--r--	root/root	usr/include/Phyl/TreeParsimonyData.h
-rw-r--r--	root/root	usr/include/Phyl/TreeParsimonyScore.h
-rw-r--r--	root/root	usr/include/Phyl/TreeTemplate.h
-rw-r--r--	root/root	usr/include/Phyl/TreeTemplateTools.h
-rw-r--r--	root/root	usr/include/Phyl/TreeTools.h
-rw-r--r--	root/root	usr/include/Phyl/TripletReversibleSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/UserProteinSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/WordReversibleSubstitutionModel.h
-rw-r--r--	root/root	usr/include/Phyl/YN98.h
-rw-r--r--	root/root	usr/include/Phyl/iodistance
-rw-r--r--	root/root	usr/include/Phyl/iotree
-rw-r--r--	root/root	usr/include/Phyl/models
-rw-r--r--	root/root	usr/include/Phyl/treelikelihoods
-rw-r--r--	root/root	usr/include/Phyl/trees
drwxr-xr-x	root/root	usr/lib/
drwxr-xr-x	root/root	usr/lib/Bpp1/
-rw-r--r--	root/root	usr/lib/Bpp1/libbpp-phyl.a
lrwxrwxrwx	root/root	usr/lib/Bpp1/libbpp-phyl.so -> libbpp-phyl.so.9
lrwxrwxrwx	root/root	usr/lib/Bpp1/libbpp-phyl.so.9 -> libbpp-phyl.so.9.0.0
-rwxr-xr-x	root/root	usr/lib/Bpp1/libbpp-phyl.so.9.0.0