MANIFEST.in
README.md
setup.py
bin/bootstrap
bin/collapse
bin/simulator
bin/treeCl
extensions/tree_collection/cython/py_wrapper.pyx
extensions/tree_collection/cython/wrapper.cpp
extensions/tree_collection/cython/wrapper.pxd
extensions/tree_collection/src/MinSqTree.cc
extensions/tree_collection/src/MinSqTree.h
extensions/tree_collection/src/PhyTree.h
extensions/tree_collection/src/ProblemParser.cc
extensions/tree_collection/src/ProblemParser.h
extensions/tree_collection/src/newick.cc
extensions/tree_collection/src/newick.h
extensions/tree_collection/src/eigen3/Eigen/Core
extensions/tree_collection/src/eigen3/Eigen/LU
extensions/tree_collection/src/eigen3/Eigen/src/Core/Array.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/ArrayBase.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/ArrayWrapper.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Assign.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Assign_MKL.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/BandMatrix.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Block.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/BooleanRedux.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/Core/CommaInitializer.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/CoreIterators.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/CwiseBinaryOp.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/CwiseNullaryOp.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/CwiseUnaryOp.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/CwiseUnaryView.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/DenseBase.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/DenseCoeffsBase.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/DenseStorage.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Diagonal.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/DiagonalMatrix.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/DiagonalProduct.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Dot.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/EigenBase.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Flagged.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/ForceAlignedAccess.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Functors.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Fuzzy.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/GeneralProduct.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/GenericPacketMath.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/GlobalFunctions.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/IO.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Map.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/MapBase.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/MathFunctions.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Matrix.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/MatrixBase.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/NestByValue.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/NoAlias.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/NumTraits.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/PermutationMatrix.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/PlainObjectBase.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/ProductBase.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Random.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Redux.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Ref.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Replicate.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/ReturnByValue.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Reverse.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Select.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/SelfAdjointView.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/SolveTriangular.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/StableNorm.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Stride.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Swap.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Transpose.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Transpositions.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/TriangularMatrix.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/VectorBlock.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/VectorwiseOp.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/Visitor.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/arch/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/Core/arch/AltiVec/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/Core/arch/AltiVec/Complex.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/arch/AltiVec/PacketMath.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/arch/Default/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/Core/arch/Default/Settings.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/arch/NEON/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/Core/arch/NEON/Complex.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/arch/SSE/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/Core/arch/SSE/Complex.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/arch/SSE/MathFunctions.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/CoeffBasedProduct.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/GeneralMatrixMatrix.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_MKL.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/GeneralMatrixMatrix_MKL.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/GeneralMatrixVector.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/GeneralMatrixVector_MKL.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/Parallelizer.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/SelfadjointMatrixMatrix.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/SelfadjointMatrixMatrix_MKL.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/SelfadjointMatrixVector.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/SelfadjointMatrixVector_MKL.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/SelfadjointProduct.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/SelfadjointRank2Update.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/TriangularMatrixMatrix.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/TriangularMatrixMatrix_MKL.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/TriangularMatrixVector_MKL.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/TriangularSolverMatrix.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/TriangularSolverMatrix_MKL.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/products/TriangularSolverVector.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/util/BlasUtil.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/util/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/Core/util/Constants.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/util/DisableStupidWarnings.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/util/ForwardDeclarations.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/util/MKL_support.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/util/Macros.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/util/Memory.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/util/Meta.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/util/NonMPL2.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/util/ReenableStupidWarnings.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/util/StaticAssert.h
extensions/tree_collection/src/eigen3/Eigen/src/Core/util/XprHelper.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Block.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Cwise.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/CwiseOperators.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/LU.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Lazy.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/LeastSquares.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Macros.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/MathFunctions.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Memory.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Meta.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Minor.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/QR.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/SVD.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/TriangularSolver.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/VectorBlock.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Geometry/AlignedBox.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Geometry/All.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Geometry/AngleAxis.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Geometry/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Geometry/Hyperplane.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Geometry/ParametrizedLine.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Geometry/Quaternion.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Geometry/Rotation2D.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Geometry/RotationBase.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Geometry/Scaling.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Geometry/Transform.h
extensions/tree_collection/src/eigen3/Eigen/src/Eigen2Support/Geometry/Translation.h
extensions/tree_collection/src/eigen3/Eigen/src/LU/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/LU/Determinant.h
extensions/tree_collection/src/eigen3/Eigen/src/LU/FullPivLU.h
extensions/tree_collection/src/eigen3/Eigen/src/LU/Inverse.h
extensions/tree_collection/src/eigen3/Eigen/src/LU/PartialPivLU.h
extensions/tree_collection/src/eigen3/Eigen/src/LU/PartialPivLU_MKL.h
extensions/tree_collection/src/eigen3/Eigen/src/LU/arch/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/LU/arch/Inverse_SSE.h
extensions/tree_collection/src/eigen3/Eigen/src/misc/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/misc/Image.h
extensions/tree_collection/src/eigen3/Eigen/src/misc/Kernel.h
extensions/tree_collection/src/eigen3/Eigen/src/misc/Solve.h
extensions/tree_collection/src/eigen3/Eigen/src/misc/SparseSolve.h
extensions/tree_collection/src/eigen3/Eigen/src/misc/blas.h
extensions/tree_collection/src/eigen3/Eigen/src/plugins/ArrayCwiseBinaryOps.h
extensions/tree_collection/src/eigen3/Eigen/src/plugins/ArrayCwiseUnaryOps.h
extensions/tree_collection/src/eigen3/Eigen/src/plugins/BlockMethods.h
extensions/tree_collection/src/eigen3/Eigen/src/plugins/CMakeLists.txt
extensions/tree_collection/src/eigen3/Eigen/src/plugins/CommonCwiseBinaryOps.h
extensions/tree_collection/src/eigen3/Eigen/src/plugins/CommonCwiseUnaryOps.h
extensions/tree_collection/src/eigen3/Eigen/src/plugins/MatrixCwiseBinaryOps.h
extensions/tree_collection/src/eigen3/Eigen/src/plugins/MatrixCwiseUnaryOps.h
tests/__init__.py
tests/test.py
tests/data/class1_1.phy
tests/data/class1_2.phy
tests/data/class1_3.phy
tests/data/class1_4.phy
tests/data/class1_5.phy
tests/data/class2_1.phy
tests/data/class2_2.phy
tests/data/class2_3.phy
tests/data/class2_4.phy
tests/data/class2_5.phy
tests/data/class3_1.phy
tests/data/class3_2.phy
tests/data/class3_3.phy
tests/data/class3_4.phy
tests/data/class3_5.phy
tests/data/cache/class1_1.json.gz
tests/data/cache/class1_2.json.gz
tests/data/cache/class1_3.json.gz
tests/data/cache/class1_4.json.gz
tests/data/cache/class1_5.json.gz
tests/data/cache/class2_1.json.gz
tests/data/cache/class2_2.json.gz
tests/data/cache/class2_3.json.gz
tests/data/cache/class2_4.json.gz
tests/data/cache/class2_5.json.gz
tests/data/cache/class3_1.json.gz
tests/data/cache/class3_2.json.gz
tests/data/cache/class3_3.json.gz
tests/data/cache/class3_4.json.gz
tests/data/cache/class3_5.json.gz
tests/data/cache/geo_dm.csv
tests/data/mini/class1_1.fas
tests/data/mini/class1_1.fas.bz2
tests/data/mini/class1_1.fas.gz
tests/data/mini/class1_1.phy
tests/data/mini/class1_1.phy.bz2
tests/data/mini/class1_1.phy.gz
tests/data/parsing/RAxML_info.modopt
tests/data/parsing/RAxML_info.modoptq
tests/data/parsing/RAxML_result.modopt
tests/data/parsing/RAxML_result.modoptq
tests/data/trees/class1_1.nwk
tests/data/trees/class1_2.nwk
tests/data/trees/class1_3.nwk
tests/data/trees/class1_4.nwk
tests/data/trees/class1_5.nwk
tests/data/trees/class2_1.nwk
tests/data/trees/class2_2.nwk
tests/data/trees/class2_3.nwk
tests/data/trees/class2_4.nwk
tests/data/trees/class2_5.nwk
tests/data/trees/class3_1.nwk
tests/data/trees/class3_2.nwk
tests/data/trees/class3_3.nwk
tests/data/trees/class3_4.nwk
tests/data/trees/class3_5.nwk
treeCl/__init__.py
treeCl/alignment.py
treeCl/bootstrap.py
treeCl/clustering.py
treeCl/collection.py
treeCl/colours.py
treeCl/concatenation.py
treeCl/constants.py
treeCl/distance_matrix.py
treeCl/errors.py
treeCl/parameters.py
treeCl/parsers.py
treeCl/partition.py
treeCl/parutils.py
treeCl/plotter.py
treeCl/simulator.py
treeCl/tasks.py
treeCl/tree.py
treeCl/treedist.py
treeCl.egg-info/PKG-INFO
treeCl.egg-info/SOURCES.txt
treeCl.egg-info/dependency_links.txt
treeCl.egg-info/requires.txt
treeCl.egg-info/top_level.txt
treeCl/logging/logging.yaml
treeCl/utils/__init__.py
treeCl/utils/ambiguate.py
treeCl/utils/decorators.py
treeCl/utils/enum.py
treeCl/utils/fileIO.py
treeCl/utils/gapmasker.py
treeCl/utils/kelley.py
treeCl/utils/kendallcolijn.py
treeCl/utils/math.py
treeCl/utils/misc.py
treeCl/utils/printing.py
treeCl/utils/silhouette.py
treeCl/utils/translator.py
treeCl/wrappers/__init__.py
treeCl/wrappers/abstract_wrapper.py
treeCl/wrappers/aligners.py
treeCl/wrappers/phylogenetics.py