MANIFEST.in
README
setup.py
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/Link/THyPhy.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/SWIGWrappers/THyPhy_py3.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/contrib/SQLite-3.8.2/shell.c
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/contrib/SQLite-3.8.2/sqlite3.c
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/_hyExecutionContext.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/alignment.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/avllist.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/avllistx.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/avllistxl.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/baseobj.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/batchlan.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/batchlan2.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/batchlanhelpers.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/batchlanruntime.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/calcnode.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/calcnode2.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/category.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/constant.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/error.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/fisher_exact.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/formula.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/fstring.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/likefunc.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/likefunc2.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/likefuncocl.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/list.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/mathobj.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/matrix.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/nexus.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/operation.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/parser.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/parser2.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/polynoml.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/regex.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/sequence.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/simplelist.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/site.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/stack.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/strings.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/trie.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/variable.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/core/variablecontainer.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/gui/preferences.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/new/bayesgraph.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/new/bayesgraph2.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/new/bgm.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/new/bgm2.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/new/scfg.cpp
/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853059576/work/hyphy-python-0.1.6/hyphy-src/src/utils/hyphyunixutils.cpp
HyPhy/__init__.py
Link/THyPhy.cpp
Link/THyPhy.h
SWIGWrappers/THyPhy_py3.cpp
SWIGWrappers/THyPhy_python.cpp
hyphy-src/.gitignore
hyphy-src/CMakeLists.txt
hyphy-src/LICENSE
hyphy-src/README.md
hyphy-src/package.json
hyphy-src/CMakeWin32/CMakeLists.txt
hyphy-src/Examples/BatchLanguage/MatrixIndexing.bf
hyphy-src/Examples/BatchLanguage/profile_test.bf
hyphy-src/Examples/Categories/definitions+MLE.bf
hyphy-src/Examples/Categories/definitions.bf
hyphy-src/Examples/Categories/definitions2.bf
hyphy-src/Examples/Categories/definitions3.bf
hyphy-src/Examples/Categories/displayFunction.bf
hyphy-src/Examples/Categories/data/aspectrin.nuc
hyphy-src/Examples/ConstraintDefinition/ReplicateConstraint1.bf
hyphy-src/Examples/ConstraintDefinition/ReplicateConstraint2.bf
hyphy-src/Examples/ConstraintDefinition/ReplicateConstraint3.bf
hyphy-src/Examples/ConstraintDefinition/shared.bf
hyphy-src/Examples/ConstraintDefinition/data/hiv.seq
hyphy-src/Examples/DataFilters/HKY852blocks.bf
hyphy-src/Examples/DataFilters/HKY852blocks2models.bf
hyphy-src/Examples/DataFilters/data/actin2.flt
hyphy-src/Examples/MoreComplexModels/ExonIntron.bf
hyphy-src/Examples/MoreComplexModels/aa.bf
hyphy-src/Examples/MoreComplexModels/Models/EI.mdl
hyphy-src/Examples/MoreComplexModels/Models/MG94x2.mdl
hyphy-src/Examples/MoreComplexModels/data/3.seq
hyphy-src/Examples/MoreComplexModels/data/stewart.aa
hyphy-src/Examples/MoreComplexModels/data/ubiq.flt
hyphy-src/Examples/SimpleAnalyses/F81.bf
hyphy-src/Examples/SimpleAnalyses/HKY85.bf
hyphy-src/Examples/SimpleAnalyses/HKY85shared.bf
hyphy-src/Examples/SimpleAnalyses/JC69.bf
hyphy-src/Examples/SimpleAnalyses/K2P.bf
hyphy-src/Examples/SimpleAnalyses/K2Pshared.bf
hyphy-src/Examples/SimpleAnalyses/Non-Rev.bf
hyphy-src/Examples/SimpleAnalyses/REV.bf
hyphy-src/Examples/SimpleAnalyses/REVshared.bf
hyphy-src/Examples/SimpleAnalyses/data/hiv.nuc
hyphy-src/Examples/SimpleConstraints/F81K81uf_relratio.bf
hyphy-src/Examples/SimpleConstraints/F81relrate.bf
hyphy-src/Examples/SimpleConstraints/F81relratio.bf
hyphy-src/Examples/SimpleConstraints/HKY85relrate.bf
hyphy-src/Examples/SimpleConstraints/HKY85relratio.bf
hyphy-src/Examples/SimpleConstraints/MolecularClockF81.bf
hyphy-src/Examples/SimpleConstraints/MolecularClockHKY85.bf
hyphy-src/Examples/SimpleConstraints/data/3.seq
hyphy-src/Examples/SimpleConstraints/data/aspectrin1.nuc
hyphy-src/Examples/SimpleConstraints/data/aspectrin2.nuc
hyphy-src/Examples/SimpleConstraints/data/molclock.seq
hyphy-src/Examples/Simulation/PBootstrapHetRates.bf
hyphy-src/Examples/Simulation/ParametricBootstrap.bf
hyphy-src/Examples/Simulation/RelativeRatePBS.bf
hyphy-src/Examples/Simulation/data/3.seq
hyphy-src/Examples/Simulation/data/hiv.nuc
hyphy-src/cmake/FindOpenCL.cmake
hyphy-src/cmake/cmake_uninstall.cmake.in
hyphy-src/contrib/cl2hdr.c
hyphy-src/contrib/SQLite-3.8.2/shell.c
hyphy-src/contrib/SQLite-3.8.2/sqlite3.c
hyphy-src/contrib/SQLite-3.8.2/sqlite3.h
hyphy-src/contrib/SQLite-3.8.2/sqlite3ext.h
hyphy-src/contrib/gtest-1.7.0/CHANGES
hyphy-src/contrib/gtest-1.7.0/CMakeLists.txt
hyphy-src/contrib/gtest-1.7.0/CONTRIBUTORS
hyphy-src/contrib/gtest-1.7.0/LICENSE
hyphy-src/contrib/gtest-1.7.0/Makefile.am
hyphy-src/contrib/gtest-1.7.0/Makefile.in
hyphy-src/contrib/gtest-1.7.0/README
hyphy-src/contrib/gtest-1.7.0/aclocal.m4
hyphy-src/contrib/gtest-1.7.0/configure
hyphy-src/contrib/gtest-1.7.0/configure.ac
hyphy-src/contrib/gtest-1.7.0/build-aux/config.guess
hyphy-src/contrib/gtest-1.7.0/build-aux/config.h.in
hyphy-src/contrib/gtest-1.7.0/build-aux/config.sub
hyphy-src/contrib/gtest-1.7.0/build-aux/depcomp
hyphy-src/contrib/gtest-1.7.0/build-aux/install-sh
hyphy-src/contrib/gtest-1.7.0/build-aux/ltmain.sh
hyphy-src/contrib/gtest-1.7.0/build-aux/missing
hyphy-src/contrib/gtest-1.7.0/cmake/internal_utils.cmake
hyphy-src/contrib/gtest-1.7.0/codegear/gtest.cbproj
hyphy-src/contrib/gtest-1.7.0/codegear/gtest.groupproj
hyphy-src/contrib/gtest-1.7.0/codegear/gtest_all.cc
hyphy-src/contrib/gtest-1.7.0/codegear/gtest_link.cc
hyphy-src/contrib/gtest-1.7.0/codegear/gtest_main.cbproj
hyphy-src/contrib/gtest-1.7.0/codegear/gtest_unittest.cbproj
hyphy-src/contrib/gtest-1.7.0/fused-src/gtest/gtest-all.cc
hyphy-src/contrib/gtest-1.7.0/fused-src/gtest/gtest.h
hyphy-src/contrib/gtest-1.7.0/fused-src/gtest/gtest_main.cc
hyphy-src/contrib/gtest-1.7.0/include/gtest/gtest-death-test.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/gtest-message.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/gtest-param-test.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/gtest-param-test.h.pump
hyphy-src/contrib/gtest-1.7.0/include/gtest/gtest-printers.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/gtest-spi.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/gtest-test-part.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/gtest-typed-test.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/gtest.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/gtest_pred_impl.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/gtest_prod.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-death-test-internal.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-filepath.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-internal.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-linked_ptr.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-param-util-generated.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-param-util-generated.h.pump
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-param-util.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-port.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-string.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-tuple.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-tuple.h.pump
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-type-util.h
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-type-util.h.pump
hyphy-src/contrib/gtest-1.7.0/m4/acx_pthread.m4
hyphy-src/contrib/gtest-1.7.0/m4/gtest.m4
hyphy-src/contrib/gtest-1.7.0/m4/libtool.m4
hyphy-src/contrib/gtest-1.7.0/m4/ltoptions.m4
hyphy-src/contrib/gtest-1.7.0/m4/ltsugar.m4
hyphy-src/contrib/gtest-1.7.0/m4/ltversion.m4
hyphy-src/contrib/gtest-1.7.0/m4/lt~obsolete.m4
hyphy-src/contrib/gtest-1.7.0/msvc/gtest-md.sln
hyphy-src/contrib/gtest-1.7.0/msvc/gtest-md.vcproj
hyphy-src/contrib/gtest-1.7.0/msvc/gtest.sln
hyphy-src/contrib/gtest-1.7.0/msvc/gtest.vcproj
hyphy-src/contrib/gtest-1.7.0/msvc/gtest_main-md.vcproj
hyphy-src/contrib/gtest-1.7.0/msvc/gtest_main.vcproj
hyphy-src/contrib/gtest-1.7.0/msvc/gtest_prod_test-md.vcproj
hyphy-src/contrib/gtest-1.7.0/msvc/gtest_prod_test.vcproj
hyphy-src/contrib/gtest-1.7.0/msvc/gtest_unittest-md.vcproj
hyphy-src/contrib/gtest-1.7.0/msvc/gtest_unittest.vcproj
hyphy-src/contrib/gtest-1.7.0/samples/prime_tables.h
hyphy-src/contrib/gtest-1.7.0/samples/sample1.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample1.h
hyphy-src/contrib/gtest-1.7.0/samples/sample10_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample1_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample2.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample2.h
hyphy-src/contrib/gtest-1.7.0/samples/sample2_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample3-inl.h
hyphy-src/contrib/gtest-1.7.0/samples/sample3_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample4.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample4.h
hyphy-src/contrib/gtest-1.7.0/samples/sample4_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample5_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample6_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample7_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample8_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample9_unittest.cc
hyphy-src/contrib/gtest-1.7.0/scripts/fuse_gtest_files.py
hyphy-src/contrib/gtest-1.7.0/scripts/gen_gtest_pred_impl.py
hyphy-src/contrib/gtest-1.7.0/scripts/gtest-config.in
hyphy-src/contrib/gtest-1.7.0/scripts/pump.py
hyphy-src/contrib/gtest-1.7.0/src/gtest-all.cc
hyphy-src/contrib/gtest-1.7.0/src/gtest-death-test.cc
hyphy-src/contrib/gtest-1.7.0/src/gtest-filepath.cc
hyphy-src/contrib/gtest-1.7.0/src/gtest-internal-inl.h
hyphy-src/contrib/gtest-1.7.0/src/gtest-port.cc
hyphy-src/contrib/gtest-1.7.0/src/gtest-printers.cc
hyphy-src/contrib/gtest-1.7.0/src/gtest-test-part.cc
hyphy-src/contrib/gtest-1.7.0/src/gtest-typed-test.cc
hyphy-src/contrib/gtest-1.7.0/src/gtest.cc
hyphy-src/contrib/gtest-1.7.0/src/gtest_main.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-death-test_ex_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-death-test_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-filepath_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-linked_ptr_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-listener_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-message_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-options_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-param-test2_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-param-test_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-param-test_test.h
hyphy-src/contrib/gtest-1.7.0/test/gtest-port_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-printers_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-test-part_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-tuple_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-typed-test2_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-typed-test_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-typed-test_test.h
hyphy-src/contrib/gtest-1.7.0/test/gtest-unittest-api_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_all_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_break_on_failure_unittest.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_break_on_failure_unittest_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_catch_exceptions_test.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_catch_exceptions_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_color_test.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_color_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_env_var_test.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_env_var_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_environment_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_filter_unittest.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_filter_unittest_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_help_test.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_help_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_list_tests_unittest.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_list_tests_unittest_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_main_unittest.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_no_test_unittest.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_output_test.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_output_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_output_test_golden_lin.txt
hyphy-src/contrib/gtest-1.7.0/test/gtest_pred_impl_unittest.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_premature_exit_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_prod_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_repeat_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_shuffle_test.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_shuffle_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_sole_header_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_stress_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_test_utils.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_throw_on_failure_ex_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_throw_on_failure_test.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_throw_on_failure_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_uninitialized_test.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_uninitialized_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_unittest.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_xml_outfile1_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_xml_outfile2_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_xml_outfiles_test.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_xml_output_unittest.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_xml_output_unittest_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_xml_test_utils.py
hyphy-src/contrib/gtest-1.7.0/test/production.cc
hyphy-src/contrib/gtest-1.7.0/test/production.h
hyphy-src/contrib/gtest-1.7.0/xcode/Config/DebugProject.xcconfig
hyphy-src/contrib/gtest-1.7.0/xcode/Config/FrameworkTarget.xcconfig
hyphy-src/contrib/gtest-1.7.0/xcode/Config/General.xcconfig
hyphy-src/contrib/gtest-1.7.0/xcode/Config/ReleaseProject.xcconfig
hyphy-src/contrib/gtest-1.7.0/xcode/Config/StaticLibraryTarget.xcconfig
hyphy-src/contrib/gtest-1.7.0/xcode/Config/TestTarget.xcconfig
hyphy-src/contrib/gtest-1.7.0/xcode/Resources/Info.plist
hyphy-src/contrib/gtest-1.7.0/xcode/Samples/FrameworkSample/Info.plist
hyphy-src/contrib/gtest-1.7.0/xcode/Samples/FrameworkSample/runtests.sh
hyphy-src/contrib/gtest-1.7.0/xcode/Samples/FrameworkSample/widget.cc
hyphy-src/contrib/gtest-1.7.0/xcode/Samples/FrameworkSample/widget.h
hyphy-src/contrib/gtest-1.7.0/xcode/Samples/FrameworkSample/widget_test.cc
hyphy-src/contrib/gtest-1.7.0/xcode/Samples/FrameworkSample/WidgetFramework.xcodeproj/project.pbxproj
hyphy-src/contrib/gtest-1.7.0/xcode/Scripts/runtests.sh
hyphy-src/contrib/gtest-1.7.0/xcode/Scripts/versiongenerate.py
hyphy-src/contrib/gtest-1.7.0/xcode/gtest.xcodeproj/project.pbxproj
hyphy-src/help/Getting Started With HyPhy.pdf
hyphy-src/help/SelectionAnalyses.pdf
hyphy-src/help/Commands/query.bf
hyphy-src/help/Commands/reference.sql
hyphy-src/installers/Mac/DMG.key
hyphy-src/installers/Mac/MAC_dmg_template.dmgCanvas/Disk Image
hyphy-src/installers/Mac/MAC_dmg_template.dmgCanvas/QuickLook/Preview.jpg
hyphy-src/installers/Win/hyphy.nsi
hyphy-src/installers/Win/license.rtf
hyphy-src/res/ChartAddIns/Approximate_CDF
hyphy-src/res/ChartAddIns/Column Operations
hyphy-src/res/ChartAddIns/Complex Select Cells By Value
hyphy-src/res/ChartAddIns/Contigency Table
hyphy-src/res/ChartAddIns/Covariance
hyphy-src/res/ChartAddIns/Descriptive Statistics
hyphy-src/res/ChartAddIns/Distribution Moments
hyphy-src/res/ChartAddIns/Gaussian Penalty Clustering
hyphy-src/res/ChartAddIns/Goodness of Fit
hyphy-src/res/ChartAddIns/Histogram
hyphy-src/res/ChartAddIns/K-Mean Clustering
hyphy-src/res/ChartAddIns/KH Resampler
hyphy-src/res/ChartAddIns/Linear Fit
hyphy-src/res/ChartAddIns/Linear Fit.orig
hyphy-src/res/ChartAddIns/Mean Profile Plot
hyphy-src/res/ChartAddIns/Median Profile Plot
hyphy-src/res/ChartAddIns/Poisson Mixture Fit
hyphy-src/res/ChartAddIns/Populate Cells
hyphy-src/res/ChartAddIns/Profile Mean Clustering
hyphy-src/res/ChartAddIns/Running Sum
hyphy-src/res/ChartAddIns/Select Cells By Index
hyphy-src/res/ChartAddIns/Select Cells By Value
hyphy-src/res/ChartAddIns/SingleColumn
hyphy-src/res/ChartAddIns/Sort
hyphy-src/res/ChartAddIns/DBAddIns/DescriptiveStats.bf
hyphy-src/res/ChartAddIns/DBAddIns/FromSQLFlatFile.bf
hyphy-src/res/ChartAddIns/DBAddIns/HY_DBW_TemplateList
hyphy-src/res/ChartAddIns/DBAddIns/ToChartWindow.bf
hyphy-src/res/ChartAddIns/DBAddIns/ToConsole.bf
hyphy-src/res/ChartAddIns/DBAddIns/ToFastaFile.bf
hyphy-src/res/ChartAddIns/DBAddIns/ToFastaFileFromPandit.bf
hyphy-src/res/ChartAddIns/DBAddIns/ToFrontierFastaFile.bf
hyphy-src/res/ChartAddIns/DBAddIns/ToSQLFlatFile.bf
hyphy-src/res/ChartAddIns/DBAddIns/ToTabFile.bf
hyphy-src/res/ChartAddIns/DistributionAddIns/Event Posteriors
hyphy-src/res/ChartAddIns/DistributionAddIns/Most Likely Class Assignment
hyphy-src/res/ChartAddIns/DistributionAddIns/Posterior Distribution
hyphy-src/res/ChartAddIns/DistributionAddIns/Posterior Moments
hyphy-src/res/ChartAddIns/DistributionAddIns/Prior Moments
hyphy-src/res/ChartAddIns/DistributionAddIns/Includes/posteriors.ibf
hyphy-src/res/ChartAddIns/Samplers/lhc.bf
hyphy-src/res/ChartAddIns/Samplers/sir.bf
hyphy-src/res/ChartAddIns/Samplers/srs.ibf
hyphy-src/res/DatapanelAddIns/Character Plot
hyphy-src/res/DatapanelAddIns/Character Plot Two
hyphy-src/res/DatapanelAddIns/Compare Subsets
hyphy-src/res/DatapanelAddIns/Sequence Plot
hyphy-src/res/DatapanelAddIns/TBD/Character Plot By Sequence
hyphy-src/res/DatapanelAddIns/ibfs/char_colors.def
hyphy-src/res/GeneticCodes/Alt_Yeast_Nuclear.cod
hyphy-src/res/GeneticCodes/Ascidian_mtDNA.cod
hyphy-src/res/GeneticCodes/Blepharisma_Nuclear.cod
hyphy-src/res/GeneticCodes/Ciliate.cod
hyphy-src/res/GeneticCodes/Echinoderm_mtDNA.cod
hyphy-src/res/GeneticCodes/Euplotid_Nuclear.cod
hyphy-src/res/GeneticCodes/Flatworm_mtDNA.cod
hyphy-src/res/GeneticCodes/Invertebrate_mtDNA.cod
hyphy-src/res/GeneticCodes/Mold_mtDNA.cod
hyphy-src/res/GeneticCodes/Thraustochytrium_mtDNA.cod
hyphy-src/res/GeneticCodes/Vertebratemtdna.cod
hyphy-src/res/GeneticCodes/Yeast_mtDNA.cod
hyphy-src/res/SubstitutionClasses/aa.bf
hyphy-src/res/SubstitutionClasses/codon.bf
hyphy-src/res/SubstitutionClasses/dinuc.bf
hyphy-src/res/SubstitutionClasses/nuc.bf
hyphy-src/res/SubstitutionClasses/AAEFV/Equal
hyphy-src/res/SubstitutionClasses/AAEFV/Estimated
hyphy-src/res/SubstitutionClasses/AAEFV/Observed In Data Set
hyphy-src/res/SubstitutionClasses/AAEFV/Observed In Partition
hyphy-src/res/SubstitutionClasses/CodonEFV/Equal
hyphy-src/res/SubstitutionClasses/CodonEFV/Observed Codon
hyphy-src/res/SubstitutionClasses/CodonEFV/Observed Nuc 3 params.
hyphy-src/res/SubstitutionClasses/CodonEFV/Observed Nuc 9 params.
hyphy-src/res/SubstitutionClasses/Heterogeneity/2 Bin Discrete
hyphy-src/res/SubstitutionClasses/Heterogeneity/Beta
hyphy-src/res/SubstitutionClasses/Heterogeneity/Beta-Gamma
hyphy-src/res/SubstitutionClasses/Heterogeneity/General Discrete
hyphy-src/res/SubstitutionClasses/Heterogeneity/Half Normal
hyphy-src/res/SubstitutionClasses/Heterogeneity/Lognormal
hyphy-src/res/SubstitutionClasses/NucEFV/Equal
hyphy-src/res/SubstitutionClasses/NucEFV/Estimated
hyphy-src/res/SubstitutionClasses/NucEFV/Observed In Data Set
hyphy-src/res/SubstitutionClasses/NucEFV/Observed In Partition
hyphy-src/res/SubstitutionModels/Aminoacid/Dayhoff.mdl
hyphy-src/res/SubstitutionModels/Aminoacid/EIAA.mdl
hyphy-src/res/SubstitutionModels/Aminoacid/Fitness.mdl
hyphy-src/res/SubstitutionModels/Aminoacid/Jones.mdl
hyphy-src/res/SubstitutionModels/Aminoacid/mtREV.mdl
hyphy-src/res/SubstitutionModels/Binary/F81.mdl
hyphy-src/res/SubstitutionModels/Codon/GY94_3x4.mdl
hyphy-src/res/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl
hyphy-src/res/SubstitutionModels/Codon/MG94.mdl
hyphy-src/res/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl
hyphy-src/res/SubstitutionModels/Codon/MG94_3x4.mdl
hyphy-src/res/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl
hyphy-src/res/SubstitutionModels/Codon/MG94_REV_3x4.mdl
hyphy-src/res/SubstitutionModels/Codon/MG94_REV_3x4.mdl copy
hyphy-src/res/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl
hyphy-src/res/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl
hyphy-src/res/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl
hyphy-src/res/SubstitutionModels/Codon/MG94xTN93_3x4.mdl
hyphy-src/res/SubstitutionModels/Nucleotide/EFVEstimated.ibf
hyphy-src/res/SubstitutionModels/Nucleotide/F81.mdl
hyphy-src/res/SubstitutionModels/Nucleotide/HKY85.mdl
hyphy-src/res/SubstitutionModels/Nucleotide/REV.mdl
hyphy-src/res/SubstitutionModels/Nucleotide/REVBetaGamma.mdl
hyphy-src/res/SubstitutionModels/Nucleotide/TrN.mdl
hyphy-src/res/SubstitutionModels/User/Nucleotide/JC69
hyphy-src/res/SubstitutionModels/User/Nucleotide/K2P
hyphy-src/res/TemplateBatchFiles/454.bf
hyphy-src/res/TemplateBatchFiles/AAModelComparison.bf
hyphy-src/res/TemplateBatchFiles/AddABias.ibf
hyphy-src/res/TemplateBatchFiles/AnalyzeCodonData.bf
hyphy-src/res/TemplateBatchFiles/AnalyzeCodonDataMPI.bf
hyphy-src/res/TemplateBatchFiles/AnalyzeDiNucData.bf
hyphy-src/res/TemplateBatchFiles/AnalyzeNucDataFreq.bf
hyphy-src/res/TemplateBatchFiles/AnalyzeNucDataFreq2.bf
hyphy-src/res/TemplateBatchFiles/AnalyzeNucProtData.bf
hyphy-src/res/TemplateBatchFiles/AnalyzeNucProtData2.bf
hyphy-src/res/TemplateBatchFiles/BGM.bf
hyphy-src/res/TemplateBatchFiles/BS2007.bf
hyphy-src/res/TemplateBatchFiles/BUSTED-SRV.bf
hyphy-src/res/TemplateBatchFiles/BUSTED.bf
hyphy-src/res/TemplateBatchFiles/BivariateCodonRateAnalysis.bf
hyphy-src/res/TemplateBatchFiles/BranchClassDNDS.bf
hyphy-src/res/TemplateBatchFiles/BranchSiteREL.bf
hyphy-src/res/TemplateBatchFiles/BranchSiteRELMultiModel.bf
hyphy-src/res/TemplateBatchFiles/BranchSwap.bf
hyphy-src/res/TemplateBatchFiles/CleanGaps.bf
hyphy-src/res/TemplateBatchFiles/CleanStopCodons.bf
hyphy-src/res/TemplateBatchFiles/ClusterAnalysis.bf
hyphy-src/res/TemplateBatchFiles/ClusterByDistanceRange.bf
hyphy-src/res/TemplateBatchFiles/CodonBivariateRateProcessor.bf
hyphy-src/res/TemplateBatchFiles/CodonModelCompare.bf
hyphy-src/res/TemplateBatchFiles/CodonToProtein.bf
hyphy-src/res/TemplateBatchFiles/CodonUsageBias.bf
hyphy-src/res/TemplateBatchFiles/CompareSelectivePressure.bf
hyphy-src/res/TemplateBatchFiles/CompareSelectivePressureIVL.bf
hyphy-src/res/TemplateBatchFiles/ConvertDataFile.bf
hyphy-src/res/TemplateBatchFiles/DatedTipsMolecularClock.bf
hyphy-src/res/TemplateBatchFiles/DirectionalREL.bf
hyphy-src/res/TemplateBatchFiles/DirectionalREL_MF.bf
hyphy-src/res/TemplateBatchFiles/DistanceMatrix.bf
hyphy-src/res/TemplateBatchFiles/DistanceMatrix_Splits.bf
hyphy-src/res/TemplateBatchFiles/FUBAR.bf
hyphy-src/res/TemplateBatchFiles/F_ST.bf
hyphy-src/res/TemplateBatchFiles/FitnessAAModels.bf
hyphy-src/res/TemplateBatchFiles/GADatedClock.bf
hyphy-src/res/TemplateBatchFiles/GADatedClock.ibf
hyphy-src/res/TemplateBatchFiles/GADatedClockProcessor.bf
hyphy-src/res/TemplateBatchFiles/GADatedClockProcessorM.bf
hyphy-src/res/TemplateBatchFiles/GARD.bf
hyphy-src/res/TemplateBatchFiles/GARDProcessor.bf
hyphy-src/res/TemplateBatchFiles/GARD_GA_CHC.ibf
hyphy-src/res/TemplateBatchFiles/GARecomb.bf
hyphy-src/res/TemplateBatchFiles/GA_CHC.ibf
hyphy-src/res/TemplateBatchFiles/GA_CHC_Binary.ibf
hyphy-src/res/TemplateBatchFiles/GA_CHC_kernel.ibf
hyphy-src/res/TemplateBatchFiles/Gateaux.bf
hyphy-src/res/TemplateBatchFiles/Gateaux2.bf
hyphy-src/res/TemplateBatchFiles/GateauxMR.bf
hyphy-src/res/TemplateBatchFiles/KHTest.bf
hyphy-src/res/TemplateBatchFiles/Kernel_PCA.bf
hyphy-src/res/TemplateBatchFiles/Kernel_k_means.bf
hyphy-src/res/TemplateBatchFiles/Kernel_support.ibf
hyphy-src/res/TemplateBatchFiles/LHT.bf
hyphy-src/res/TemplateBatchFiles/LRTRecombTest.bf
hyphy-src/res/TemplateBatchFiles/LZ_Complexity.bf
hyphy-src/res/TemplateBatchFiles/LocalBranchSiteTest.bf
hyphy-src/res/TemplateBatchFiles/LocalMolClock.bf
hyphy-src/res/TemplateBatchFiles/MEDS.bf
hyphy-src/res/TemplateBatchFiles/MEME_mf.bf
hyphy-src/res/TemplateBatchFiles/MFPSreader.def
hyphy-src/res/TemplateBatchFiles/MFPositiveSelection.bf
hyphy-src/res/TemplateBatchFiles/MFPositiveSelectionPooled.bf
hyphy-src/res/TemplateBatchFiles/MGvsGY.bf
hyphy-src/res/TemplateBatchFiles/MaxChi2.bf
hyphy-src/res/TemplateBatchFiles/MergeSequences.bf
hyphy-src/res/TemplateBatchFiles/MergeSites.bf
hyphy-src/res/TemplateBatchFiles/ModelSelectorAAProcessor.bf
hyphy-src/res/TemplateBatchFiles/ModelSelectorBranch.bf
hyphy-src/res/TemplateBatchFiles/ModelSelectorCodon.bf
hyphy-src/res/TemplateBatchFiles/ModelSelectorCodon.ibf
hyphy-src/res/TemplateBatchFiles/ModelSelectorCodonProcessor.bf
hyphy-src/res/TemplateBatchFiles/ModelSelectorRNA.bf
hyphy-src/res/TemplateBatchFiles/ModelSelectorRNA_1.bf
hyphy-src/res/TemplateBatchFiles/ModelTest.bf
hyphy-src/res/TemplateBatchFiles/MolClockAllRoots.bf
hyphy-src/res/TemplateBatchFiles/MolecularClock.bf
hyphy-src/res/TemplateBatchFiles/NeighborJoining.bf
hyphy-src/res/TemplateBatchFiles/NielsenYang.bf
hyphy-src/res/TemplateBatchFiles/NucModelCompare.bf
hyphy-src/res/TemplateBatchFiles/PARRIS.bf
hyphy-src/res/TemplateBatchFiles/PairwiseDNDS.bf
hyphy-src/res/TemplateBatchFiles/PairwiseRelativeRate.bf
hyphy-src/res/TemplateBatchFiles/PairwiseRelativeRatio.bf
hyphy-src/res/TemplateBatchFiles/PairwiseSiteDiversity.bf
hyphy-src/res/TemplateBatchFiles/PartitionDataFile.bf
hyphy-src/res/TemplateBatchFiles/PartitionRateComparison.bf
hyphy-src/res/TemplateBatchFiles/Phylohandbook.bf
hyphy-src/res/TemplateBatchFiles/Plato.bf
hyphy-src/res/TemplateBatchFiles/PositiveSelectionLI.bf
hyphy-src/res/TemplateBatchFiles/QuickSelectionDetection.bf
hyphy-src/res/TemplateBatchFiles/QuickSelectionDetectionMF.bf
hyphy-src/res/TemplateBatchFiles/RELAX.bf
hyphy-src/res/TemplateBatchFiles/RateClassCounter.bf
hyphy-src/res/TemplateBatchFiles/ReduceDataSetMatrix.bf
hyphy-src/res/TemplateBatchFiles/RelativeRate.bf
hyphy-src/res/TemplateBatchFiles/RelativeRateL.bf
hyphy-src/res/TemplateBatchFiles/RelativeRatio.bf
hyphy-src/res/TemplateBatchFiles/SGASimProcessor.bf
hyphy-src/res/TemplateBatchFiles/SGEmulator.bf
hyphy-src/res/TemplateBatchFiles/SGEmulator_MF.bf
hyphy-src/res/TemplateBatchFiles/SGIvL.bf
hyphy-src/res/TemplateBatchFiles/SSRatesTest.bf
hyphy-src/res/TemplateBatchFiles/SampleProcessor.bf
hyphy-src/res/TemplateBatchFiles/SandNSAmbigs.bf
hyphy-src/res/TemplateBatchFiles/SelectionLRT.bf
hyphy-src/res/TemplateBatchFiles/SeqAlignShared.ibf
hyphy-src/res/TemplateBatchFiles/SeqAlignment.bf
hyphy-src/res/TemplateBatchFiles/SeqAlignmentCodon.bf
hyphy-src/res/TemplateBatchFiles/SeqAlignmentCodonShared.ibf
hyphy-src/res/TemplateBatchFiles/SeqAlignmentNuc.bf
hyphy-src/res/TemplateBatchFiles/SeqAlignmentNucShared.ibf
hyphy-src/res/TemplateBatchFiles/SeqAlignmentProt.bf
hyphy-src/res/TemplateBatchFiles/SeqAlignmentTop75.bf
hyphy-src/res/TemplateBatchFiles/SequentialAddition.bf
hyphy-src/res/TemplateBatchFiles/SequentialAddition.ibf
hyphy-src/res/TemplateBatchFiles/SimilarityPlot.bf
hyphy-src/res/TemplateBatchFiles/SimmondsAI.bf
hyphy-src/res/TemplateBatchFiles/SimpleMutationCounter.bf
hyphy-src/res/TemplateBatchFiles/SingleBreakpointRecomb-2.bf
hyphy-src/res/TemplateBatchFiles/SingleBreakpointRecomb.bf
hyphy-src/res/TemplateBatchFiles/SiteRates.bf
hyphy-src/res/TemplateBatchFiles/SiteRates2.bf
hyphy-src/res/TemplateBatchFiles/SlatkinMaddison-2parts.bf
hyphy-src/res/TemplateBatchFiles/SlatkinMaddison.bf
hyphy-src/res/TemplateBatchFiles/SlidingNucWindow.bf
hyphy-src/res/TemplateBatchFiles/SlidingWindowAnalysis.bf
hyphy-src/res/TemplateBatchFiles/SplitSequencesByPattern.bf
hyphy-src/res/TemplateBatchFiles/StarDecomposition.bf
hyphy-src/res/TemplateBatchFiles/StrandGRMTest.bf
hyphy-src/res/TemplateBatchFiles/StripStopCodons.bf
hyphy-src/res/TemplateBatchFiles/SubtreeSelectionComparison.bf
hyphy-src/res/TemplateBatchFiles/TestBranchDNDS.bf
hyphy-src/res/TemplateBatchFiles/TestClade.bf
hyphy-src/res/TemplateBatchFiles/TestCladeMeans.bf
hyphy-src/res/TemplateBatchFiles/TopologySearch.bf
hyphy-src/res/TemplateBatchFiles/TopologySearchConstrained.bf
hyphy-src/res/TemplateBatchFiles/TreeCorrelationCoefficients.bf
hyphy-src/res/TemplateBatchFiles/TreeTools.ibf
hyphy-src/res/TemplateBatchFiles/UpperBound.bf
hyphy-src/res/TemplateBatchFiles/WANC.bf
hyphy-src/res/TemplateBatchFiles/WebUpdate.bf
hyphy-src/res/TemplateBatchFiles/YangNielsenBranchSite2005.bf
hyphy-src/res/TemplateBatchFiles/_BMS_Aux.ibf
hyphy-src/res/TemplateBatchFiles/_CMS_Aux.ibf
hyphy-src/res/TemplateBatchFiles/_MFReader_.ibf
hyphy-src/res/TemplateBatchFiles/_MSCOneStep.ibf
hyphy-src/res/TemplateBatchFiles/_tipDater.ibf
hyphy-src/res/TemplateBatchFiles/bayesgraph.ibf
hyphy-src/res/TemplateBatchFiles/binomial.ibf
hyphy-src/res/TemplateBatchFiles/branchSwappingFunctions.bf
hyphy-src/res/TemplateBatchFiles/categoryEcho.bf
hyphy-src/res/TemplateBatchFiles/chooseDistanceFormula.def
hyphy-src/res/TemplateBatchFiles/dNdSBivariateRateAnalysis.bf
hyphy-src/res/TemplateBatchFiles/dNdSBivariateRateAnalysis_CompareDS.bf
hyphy-src/res/TemplateBatchFiles/dNdSDistributionComparison.bf
hyphy-src/res/TemplateBatchFiles/dNdSDistributionComparisonMF.bf
hyphy-src/res/TemplateBatchFiles/dNdSDistributionComparisonPartitions.bf
hyphy-src/res/TemplateBatchFiles/dNdSRateAnalysis.bf
hyphy-src/res/TemplateBatchFiles/dNdSRateAnalysis_MF.bf
hyphy-src/res/TemplateBatchFiles/dNdSResultProcessor.bf
hyphy-src/res/TemplateBatchFiles/dSdNTreeTools.ibf
hyphy-src/res/TemplateBatchFiles/distanceMethodNPBootstrap.bf
hyphy-src/res/TemplateBatchFiles/distanceRMethodNPBootstrap.bf
hyphy-src/res/TemplateBatchFiles/doNNISwap.bf
hyphy-src/res/TemplateBatchFiles/doSPRSwap.bf
hyphy-src/res/TemplateBatchFiles/files.lst
hyphy-src/res/TemplateBatchFiles/globalChecker.ibf
hyphy-src/res/TemplateBatchFiles/heuristicMethodNPBootstrap.bf
hyphy-src/res/TemplateBatchFiles/last.date
hyphy-src/res/TemplateBatchFiles/molclockBootstrap.bf
hyphy-src/res/TemplateBatchFiles/pairwiseDistanceEstimator.ibf
hyphy-src/res/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf
hyphy-src/res/TemplateBatchFiles/partitionSequences.ibf
hyphy-src/res/TemplateBatchFiles/post_ancestors.bf
hyphy-src/res/TemplateBatchFiles/post_counting.bf
hyphy-src/res/TemplateBatchFiles/post_covariance.bf
hyphy-src/res/TemplateBatchFiles/post_dNdS.bf
hyphy-src/res/TemplateBatchFiles/post_lfprofile.bf
hyphy-src/res/TemplateBatchFiles/post_npbs.bf
hyphy-src/res/TemplateBatchFiles/post_pbs.bf
hyphy-src/res/TemplateBatchFiles/post_sampler.bf
hyphy-src/res/TemplateBatchFiles/post_saveResults.bf
hyphy-src/res/TemplateBatchFiles/post_sns.bf
hyphy-src/res/TemplateBatchFiles/post_variance.bf
hyphy-src/res/TemplateBatchFiles/post_viewResults.bf
hyphy-src/res/TemplateBatchFiles/postprocessors.lst
hyphy-src/res/TemplateBatchFiles/qndhelper1.ibf
hyphy-src/res/TemplateBatchFiles/qndhelper1_mf.ibf
hyphy-src/res/TemplateBatchFiles/qndhelper2.ibf
hyphy-src/res/TemplateBatchFiles/qndhelper2_mf.ibf
hyphy-src/res/TemplateBatchFiles/qndhelper3.ibf
hyphy-src/res/TemplateBatchFiles/qndhelper4.ibf
hyphy-src/res/TemplateBatchFiles/queryTree.bf
hyphy-src/res/TemplateBatchFiles/readIndexFile.bf
hyphy-src/res/TemplateBatchFiles/relrateBootstrap.bf
hyphy-src/res/TemplateBatchFiles/relrateBootstrapL.bf
hyphy-src/res/TemplateBatchFiles/relratioBootstrap.bf
hyphy-src/res/TemplateBatchFiles/selectModelParameters.bf
hyphy-src/res/TemplateBatchFiles/simpleBootstrap.bf
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/GY94.mdl
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/gamma1.def
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def
hyphy-src/res/TemplateBatchFiles/2RatesAnalyses/gamma2.def
hyphy-src/res/TemplateBatchFiles/Distances/CodonTools.def
hyphy-src/res/TemplateBatchFiles/Distances/CodonTools2.def
hyphy-src/res/TemplateBatchFiles/Distances/CodonToolsMain.def
hyphy-src/res/TemplateBatchFiles/Distances/JC69
hyphy-src/res/TemplateBatchFiles/Distances/K2P
hyphy-src/res/TemplateBatchFiles/Distances/K2P_RV
hyphy-src/res/TemplateBatchFiles/Distances/Modified_Nei_Gojobori
hyphy-src/res/TemplateBatchFiles/Distances/Nei_Gojobori
hyphy-src/res/TemplateBatchFiles/Distances/PC
hyphy-src/res/TemplateBatchFiles/Distances/PC_MH
hyphy-src/res/TemplateBatchFiles/Distances/PC_RV
hyphy-src/res/TemplateBatchFiles/Distances/T3P
hyphy-src/res/TemplateBatchFiles/Distances/TN84
hyphy-src/res/TemplateBatchFiles/Distances/TN93
hyphy-src/res/TemplateBatchFiles/Distances/TN93_RV
hyphy-src/res/TemplateBatchFiles/Distances/Unaligned_LZ
hyphy-src/res/TemplateBatchFiles/Distances/Unaligned_LZ_FR
hyphy-src/res/TemplateBatchFiles/Distances/p_Distance
hyphy-src/res/TemplateBatchFiles/Distances/p_Distance_aa
hyphy-src/res/TemplateBatchFiles/Distances/p_Distance_binary
hyphy-src/res/TemplateBatchFiles/Distances/p_Distance_codon
hyphy-src/res/TemplateBatchFiles/FUBAR_HBL/FUBAR_PHASE_1.bf
hyphy-src/res/TemplateBatchFiles/FUBAR_HBL/FUBAR_PHASE_2.bf
hyphy-src/res/TemplateBatchFiles/FUBAR_HBL/FUBAR_PHASE_3.bf
hyphy-src/res/TemplateBatchFiles/FUBAR_HBL/FUBAR_PHASE_4.bf
hyphy-src/res/TemplateBatchFiles/FUBAR_HBL/FUBAR_PHASE_5.bf
hyphy-src/res/TemplateBatchFiles/FUBAR_HBL/FUBAR_tools.ibf
hyphy-src/res/TemplateBatchFiles/GUI/crayolaColors.def
hyphy-src/res/TemplateBatchFiles/Samplers/lhc.bf
hyphy-src/res/TemplateBatchFiles/Samplers/lhc_supp.ibf
hyphy-src/res/TemplateBatchFiles/Samplers/sir.bf
hyphy-src/res/TemplateBatchFiles/Samplers/srs.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/190
hyphy-src/res/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/CF3x4.bf
hyphy-src/res/TemplateBatchFiles/TemplateModels/Custom_AA.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Dayhoff.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Default
hyphy-src/res/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/ECM+F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/ECM.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/EIAA.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/EX.dat
hyphy-src/res/TemplateBatchFiles/TemplateModels/EX.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/F81.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/F81_binary.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/F84.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/F84P.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/GRM.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/GY94.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/GY94.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/GY94w9.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVbetween.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVbetween.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVwithin.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVwithin.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/HKY85.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/JC69.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/JC69_binary.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Jones.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Jones_F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/K2P.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/K3ST.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/LCAP.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MEC.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94custom.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94wAA.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94wAAF61multiple.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94wAAFreqs.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94wEX.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94x2.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/MGwAA.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/MGwEX.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/NRM.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/PCH
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNA16.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNA16A
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNAEqualInput
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNAF81
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNAREV
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNAREV_1
hyphy-src/res/TemplateBatchFiles/TemplateModels/S4
hyphy-src/res/TemplateBatchFiles/TemplateModels/STGRM.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/TrN.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/UniversalCode.def
hyphy-src/res/TemplateBatchFiles/TemplateModels/WAG.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/WAG_F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def
hyphy-src/res/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def
hyphy-src/res/TemplateBatchFiles/TemplateModels/custm4x4.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/defineGamma.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/defineHM.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/fitness.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/modelParameters.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/modelParameters2.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/modelParameters3.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/modelParameters4.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/modelParameters5.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/models.lst
hyphy-src/res/TemplateBatchFiles/TemplateModels/mtMAM.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/mtREV.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/mtREV_24.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/mtREV_24_F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/reducedREV.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/rtREV.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/rtREV_F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu
hyphy-src/res/TemplateBatchFiles/Utility/AncestralMapper.bf
hyphy-src/res/TemplateBatchFiles/Utility/BranchLengthFitters.bf
hyphy-src/res/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf
hyphy-src/res/TemplateBatchFiles/Utility/CodonTools.bf
hyphy-src/res/TemplateBatchFiles/Utility/DBTools.ibf
hyphy-src/res/TemplateBatchFiles/Utility/DescriptiveStatistics.bf
hyphy-src/res/TemplateBatchFiles/Utility/GrabBag.bf
hyphy-src/res/TemplateBatchFiles/Utility/HXB2Mapper.bf
hyphy-src/res/TemplateBatchFiles/Utility/LocalMGREV.bf
hyphy-src/res/TemplateBatchFiles/Utility/LocalMGREVMLFreqs.bf
hyphy-src/res/TemplateBatchFiles/Utility/MPITools.bf
hyphy-src/res/TemplateBatchFiles/Utility/NJ.bf
hyphy-src/res/TemplateBatchFiles/Utility/PS_Plotters.bf
hyphy-src/res/TemplateBatchFiles/Utility/PostScript.bf
hyphy-src/res/TemplateBatchFiles/Utility/ProbabilityDistributions.bf
hyphy-src/res/TemplateBatchFiles/Utility/ReadDelimitedFiles.bf
hyphy-src/res/TemplateBatchFiles/Utility/TreeFunctions.bf
hyphy-src/res/TemplateBatchFiles/Utility/WriteDelimitedFiles.bf
hyphy-src/res/TemplateBatchFiles/lib2014/IOFunctions.bf
hyphy-src/res/TemplateBatchFiles/lib2014/UtilityFunctions.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/DNA.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/codon.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/frequencies.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/model_functions.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/parameters.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/rate_variation.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/terms.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/DNA/GTR.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/codon/MG_REV.bf
hyphy-src/res/TemplateBatchFiles/lib2014/tasks/estimators.bf
hyphy-src/res/TopologyInference/Exhaustive_Search
hyphy-src/res/TopologyInference/Neighbor_Joining
hyphy-src/res/TopologyInference/Sequential_Addition
hyphy-src/res/TopologyInference/Star_Decomposition
hyphy-src/res/TopologyInference/Support/branchSwappingFunctions.bf
hyphy-src/res/TopologyInference/Support/doNNISwap.bf
hyphy-src/res/TopologyInference/Support/doSPRSwap.bf
hyphy-src/res/TreeAddIns/Splits
hyphy-src/res/TreeAddIns/Tree Statistics
hyphy-src/res/UserAddins/AAContent
hyphy-src/res/UserAddins/BatchFileByURL
hyphy-src/res/UserAddins/BranchLengthCI
hyphy-src/res/UserAddins/CodonMutationToTreeMapper
hyphy-src/res/UserAddins/CountSubstitutions
hyphy-src/res/UserAddins/ExportLikelihoodFunction
hyphy-src/res/UserAddins/GenBankSequences
hyphy-src/res/UserAddins/LRT
hyphy-src/res/UserAddins/ListUserFunctions
hyphy-src/res/UserAddins/MapSubstitutions
hyphy-src/res/UserAddins/MeanPairwiseDivergence
hyphy-src/res/UserAddins/MeanPairwiseDivergenceSubset
hyphy-src/res/UserAddins/ModelCounter
hyphy-src/res/UserAddins/RecombinationProcessor.bf
hyphy-src/res/UserAddins/SimulateFromLF
hyphy-src/res/UserAddins/Tidbits
hyphy-src/res/UserAddins/Includes/ChooseALF.ibf
hyphy-src/res/UserAddins/Includes/MappersHelp.ibf
hyphy-src/res/UserAddins/Includes/MappersHelpAA.ibf
hyphy-src/res/UserAddins/OldAddins/AAMutationCounter
hyphy-src/res/UserAddins/OldAddins/CodonMutationToTreeMapper.bf
hyphy-src/res/UserAddins/OldAddins/ColorPSTree
hyphy-src/res/UserAddins/OldAddins/ConvergentAndParallel
hyphy-src/res/UserAddins/OldAddins/CopyBranchLengths
hyphy-src/res/UserAddins/OldAddins/DashPSTree
hyphy-src/res/UserAddins/OldAddins/ExpsPerDirection
hyphy-src/res/UserAddins/OldAddins/FilterAssignments
hyphy-src/res/UserAddins/OldAddins/InferredAASubstitutionsCounter
hyphy-src/res/UserAddins/OldAddins/LocaldNdS
hyphy-src/res/UserAddins/OldAddins/ModelFitSummary
hyphy-src/res/UserAddins/OldAddins/ModelFitSummaryAA
hyphy-src/res/UserAddins/OldAddins/Multiclass DN DS inference
hyphy-src/res/UserAddins/OldAddins/PartitionBranchesByClasses
hyphy-src/res/UserAddins/OldAddins/PredictivePosteriorP
hyphy-src/res/UserAddins/OldAddins/RNARateMatrix
hyphy-src/res/UserAddins/OldAddins/SimulateAndTabDN_DS
hyphy-src/res/UserAddins/OldAddins/SimulateFromLF
hyphy-src/res/UserAddins/OldAddins/TreeLengthConstraint
hyphy-src/res/UserAddins/OldAddins/dNanddSTrees.bf
hyphy-src/res/UserAddins/OldAddins/dS and dN factors
hyphy-src/res/data/brown.nuc
hyphy-src/res/data/integrase_BDA.nex
hyphy-src/res/data/p51.aa
hyphy-src/res/data/p51.nex
hyphy-src/scripts/build.sh
hyphy-src/scripts/buildFromSVN.sh
hyphy-src/scripts/buildMinGWFromSVN.sh
hyphy-src/scripts/build_mingw.sh
hyphy-src/scripts/build_mingw_MEGA.sh
hyphy-src/scripts/build_mingw_gui.sh
hyphy-src/scripts/gtk_build.sh
hyphy-src/scripts/intelCCbuild.sh
hyphy-src/src/core/_hyExecutionContext.cpp
hyphy-src/src/core/alignment.cpp
hyphy-src/src/core/avllist.cpp
hyphy-src/src/core/avllistx.cpp
hyphy-src/src/core/avllistxl.cpp
hyphy-src/src/core/baseobj.cpp
hyphy-src/src/core/batchlan.cpp
hyphy-src/src/core/batchlan2.cpp
hyphy-src/src/core/batchlanhelpers.cpp
hyphy-src/src/core/batchlanruntime.cpp
hyphy-src/src/core/calcnode.cpp
hyphy-src/src/core/calcnode2.cpp
hyphy-src/src/core/category.cpp
hyphy-src/src/core/classes.cp
hyphy-src/src/core/constant.cpp
hyphy-src/src/core/error.cpp
hyphy-src/src/core/fisher_exact.cpp
hyphy-src/src/core/formula.cpp
hyphy-src/src/core/fstring.cpp
hyphy-src/src/core/likefunc.cpp
hyphy-src/src/core/likefunc2.cpp
hyphy-src/src/core/likefuncocl.cpp
hyphy-src/src/core/list.cpp
hyphy-src/src/core/mathobj.cpp
hyphy-src/src/core/matrix.cpp
hyphy-src/src/core/nexus.cpp
hyphy-src/src/core/operation.cpp
hyphy-src/src/core/parser.cpp
hyphy-src/src/core/parser2.cpp
hyphy-src/src/core/polynoml.cpp
hyphy-src/src/core/ptr_array.cp
hyphy-src/src/core/regex.cpp
hyphy-src/src/core/sequence.cpp
hyphy-src/src/core/simplelist.cpp
hyphy-src/src/core/site.cpp
hyphy-src/src/core/stack.cpp
hyphy-src/src/core/strings.cpp
hyphy-src/src/core/trie.cpp
hyphy-src/src/core/variable.cpp
hyphy-src/src/core/variablecontainer.cpp
hyphy-src/src/core/include/_hyExecutionContext.h
hyphy-src/src/core/include/alignment.h
hyphy-src/src/core/include/avllist.h
hyphy-src/src/core/include/avllistx.h
hyphy-src/src/core/include/avllistxl.h
hyphy-src/src/core/include/baseobj.h
hyphy-src/src/core/include/batchlan.h
hyphy-src/src/core/include/calcnode.h
hyphy-src/src/core/include/category.h
hyphy-src/src/core/include/classes.h
hyphy-src/src/core/include/constant.h
hyphy-src/src/core/include/defines.h
hyphy-src/src/core/include/errorfns.h
hyphy-src/src/core/include/formula.h
hyphy-src/src/core/include/fstring.h
hyphy-src/src/core/include/gnuregex.h
hyphy-src/src/core/include/hy_strings.h
hyphy-src/src/core/include/likefunc.h
hyphy-src/src/core/include/list.h
hyphy-src/src/core/include/mathobj.h
hyphy-src/src/core/include/matrix.h
hyphy-src/src/core/include/mypthread.h
hyphy-src/src/core/include/operation.h
hyphy-src/src/core/include/parser.h
hyphy-src/src/core/include/polynoml.h
hyphy-src/src/core/include/sequence.h
hyphy-src/src/core/include/simplelist.h
hyphy-src/src/core/include/site.h
hyphy-src/src/core/include/stack.h
hyphy-src/src/core/include/trie.h
hyphy-src/src/core/include/variable.h
hyphy-src/src/core/include/variablecontainer.h
hyphy-src/src/gui/HYBaseGUI.cpp
hyphy-src/src/gui/HYChartWindow.cpp
hyphy-src/src/gui/HYComponent.cpp
hyphy-src/src/gui/HYConsoleWindow.cpp
hyphy-src/src/gui/HYDBWindow.cpp
hyphy-src/src/gui/HYDataPanel.cpp
hyphy-src/src/gui/HYDialogDefs.cpp
hyphy-src/src/gui/HYEventTypes.cpp
hyphy-src/src/gui/HYGraphicPane.cpp
hyphy-src/src/gui/HYModelWindow.cpp
hyphy-src/src/gui/HYObjectInspector.cpp
hyphy-src/src/gui/HYParameterTable.cpp
hyphy-src/src/gui/HYSharedMain.cpp
hyphy-src/src/gui/HYTreePanel.cpp
hyphy-src/src/gui/HYWindow.cpp
hyphy-src/src/gui/preferences.cpp
hyphy-src/src/gui/Components/HYButton.cpp
hyphy-src/src/gui/Components/HYButtonBar.cpp
hyphy-src/src/gui/Components/HYCheckBox.cpp
hyphy-src/src/gui/Components/HYLabel.cpp
hyphy-src/src/gui/Components/HYPullDown.cpp
hyphy-src/src/gui/Components/HYSequencePanel.cpp
hyphy-src/src/gui/Components/HYTable.cpp
hyphy-src/src/gui/Components/HYTextBox.cpp
hyphy-src/src/gui/gtk/HYPlatformComponent.cpp
hyphy-src/src/gui/gtk/HYPlatformGraphicPane.cpp
hyphy-src/src/gui/gtk/HYPlatformUtils.cpp
hyphy-src/src/gui/gtk/HYPlatformWindow.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformButton.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformButtonBar.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformCheckBox.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformLabel.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformPullDown.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformSequencePane.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformTable.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformTextBox.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformBootsrapWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformChartWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformConsoleWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformDBWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformDataPanel.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformGWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformModelWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformPWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformParameterTable.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformTWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformTreePanel.cpp
hyphy-src/src/gui/gtk/include/HYPlatformComponent.h
hyphy-src/src/gui/gtk/include/HYPlatformGraphicPane.h
hyphy-src/src/gui/gtk/include/HYPlatformWindow.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformButton.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformButtonBar.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformCheckbox.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformLabel.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformPullDown.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformTable.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformTextbox.h
hyphy-src/src/gui/include/HYBaseGUI.h
hyphy-src/src/gui/include/HYDialogs.h
hyphy-src/src/gui/include/HYEventTypes.h
hyphy-src/src/gui/include/HYGraphicPane.h
hyphy-src/src/gui/include/HYObjectInspector.h
hyphy-src/src/gui/include/HYSharedMain.h
hyphy-src/src/gui/include/HYTableWindow.h
hyphy-src/src/gui/include/HYUtils.h
hyphy-src/src/gui/include/HYWindow.h
hyphy-src/src/gui/include/preferences.h
hyphy-src/src/gui/include/shared_main.h
hyphy-src/src/gui/include/Components/HYButton.h
hyphy-src/src/gui/include/Components/HYButtonBar.h
hyphy-src/src/gui/include/Components/HYCanvas.h
hyphy-src/src/gui/include/Components/HYComponent.h
hyphy-src/src/gui/include/Components/HYLabel.h
hyphy-src/src/gui/include/Components/HYList.h
hyphy-src/src/gui/include/Components/HYPullDown.h
hyphy-src/src/gui/include/Components/HYSequencePanel.h
hyphy-src/src/gui/include/Components/HYTableComponent.h
hyphy-src/src/gui/include/Components/HYTextBox.h
hyphy-src/src/gui/include/WindowClasses/HYChartWindow.h
hyphy-src/src/gui/include/WindowClasses/HYConsoleWindow.h
hyphy-src/src/gui/include/WindowClasses/HYDBWindow.h
hyphy-src/src/gui/include/WindowClasses/HYDataPanel.h
hyphy-src/src/gui/include/WindowClasses/HYGWindow.h
hyphy-src/src/gui/include/WindowClasses/HYModelWindow.h
hyphy-src/src/gui/include/WindowClasses/HYParameterTable.h
hyphy-src/src/gui/include/WindowClasses/HYTreePanel.h
hyphy-src/src/gui/mac/Docs.icns
hyphy-src/src/gui/mac/HYPHY.icns
hyphy-src/src/gui/mac/HYPHYMP.icns
hyphy-src/src/gui/mac/HYPlatformComponent.cpp
hyphy-src/src/gui/mac/HYPlatformGraphicPane.cpp
hyphy-src/src/gui/mac/HYPlatformUtils.cpp
hyphy-src/src/gui/mac/HYPlatformWindow.cpp
hyphy-src/src/gui/mac/HyPhy.rsrc
hyphy-src/src/gui/mac/Info.plist
hyphy-src/src/gui/mac/hydialogs.cpp
hyphy-src/src/gui/mac/iHyPhyDebug.rsrc
hyphy-src/src/gui/mac/plist.r
hyphy-src/src/gui/mac/plist.xml
hyphy-src/src/gui/mac/plistmp.r
hyphy-src/src/gui/mac/Components/HYPlatformButton.cpp
hyphy-src/src/gui/mac/Components/HYPlatformButtonBar.cpp
hyphy-src/src/gui/mac/Components/HYPlatformCheckBox.cpp
hyphy-src/src/gui/mac/Components/HYPlatformLabel.cpp
hyphy-src/src/gui/mac/Components/HYPlatformList.cpp
hyphy-src/src/gui/mac/Components/HYPlatformPullDown.cpp
hyphy-src/src/gui/mac/Components/HYPlatformSequencePane.cpp
hyphy-src/src/gui/mac/Components/HYPlatformTable.cpp
hyphy-src/src/gui/mac/Components/HYPlatformTextBox.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformBootsrapWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformChartWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformConsoleWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformDBWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformDataPanel.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformGWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformModelWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformPWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformParameterTable.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformTWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformTreePanel.cpp
hyphy-src/src/gui/mac/include/HYPlatformButtonMenu.h
hyphy-src/src/gui/mac/include/HYPlatformComponent.h
hyphy-src/src/gui/mac/include/HYPlatformGraphicPane.h
hyphy-src/src/gui/mac/include/HYPlatformWindow.h
hyphy-src/src/gui/mac/include/Components/HYPlatformButton.h
hyphy-src/src/gui/mac/include/Components/HYPlatformButtonBar.h
hyphy-src/src/gui/mac/include/Components/HYPlatformCheckbox.h
hyphy-src/src/gui/mac/include/Components/HYPlatformLabel.h
hyphy-src/src/gui/mac/include/Components/HYPlatformList.h
hyphy-src/src/gui/mac/include/Components/HYPlatformPullDown.h
hyphy-src/src/gui/mac/include/Components/HYPlatformTable.h
hyphy-src/src/gui/mac/include/Components/HYPlatformTextbox.h
hyphy-src/src/gui/qt/helpers.cpp
hyphy-src/src/gui/qt/hyphy_qt_utility.cpp
hyphy-src/src/gui/qt/hyphyevents.cpp
hyphy-src/src/gui/qt/hyphyhierarchicalselector.cpp
hyphy-src/src/gui/qt/hyphymain.cpp
hyphy-src/src/gui/qt/hyphymessageoutput.cpp
hyphy-src/src/gui/qt/main.cpp
hyphy-src/src/gui/qt/qterminal.cpp
hyphy-src/src/gui/qt/simplerequest.cpp
hyphy-src/src/gui/qt/include/hyphy_qt_helpers.h
hyphy-src/src/gui/qt/include/hyphyevents.h
hyphy-src/src/gui/qt/include/hyphyhierarchicalselector.h
hyphy-src/src/gui/qt/include/hyphymain.h
hyphy-src/src/gui/qt/include/hyphymessageoutput.h
hyphy-src/src/gui/qt/include/qterminal.h
hyphy-src/src/gui/qt/include/simplerequest.h
hyphy-src/src/gui/qt/ui/hyphyhierarchicalselector.ui
hyphy-src/src/gui/qt/ui/hyphymain.ui
hyphy-src/src/gui/qt/ui/hyphymessageoutput.ui
hyphy-src/src/gui/res/GTKResources/130.png
hyphy-src/src/gui/res/GTKResources/131.png
hyphy-src/src/gui/res/GTKResources/132.png
hyphy-src/src/gui/res/GTKResources/133.png
hyphy-src/src/gui/res/GTKResources/4000.png
hyphy-src/src/gui/res/GTKResources/4000.xpm
hyphy-src/src/gui/res/GTKResources/4001.png
hyphy-src/src/gui/res/GTKResources/4001.xpm
hyphy-src/src/gui/res/GTKResources/4002.png
hyphy-src/src/gui/res/GTKResources/4002.xpm
hyphy-src/src/gui/res/GTKResources/4003.png
hyphy-src/src/gui/res/GTKResources/4003.xpm
hyphy-src/src/gui/res/GTKResources/4011.png
hyphy-src/src/gui/res/GTKResources/4020.png
hyphy-src/src/gui/res/GTKResources/5000.png
hyphy-src/src/gui/res/GTKResources/5001.png
hyphy-src/src/gui/res/GTKResources/5002.png
hyphy-src/src/gui/res/GTKResources/5003.png
hyphy-src/src/gui/res/GTKResources/5004.png
hyphy-src/src/gui/res/GTKResources/5005.png
hyphy-src/src/gui/res/GTKResources/5006.png
hyphy-src/src/gui/res/GTKResources/5007.png
hyphy-src/src/gui/res/GTKResources/5020.png
hyphy-src/src/gui/res/GTKResources/6000.png
hyphy-src/src/gui/res/GTKResources/6001.png
hyphy-src/src/gui/res/GTKResources/6002.png
hyphy-src/src/gui/res/GTKResources/6003.png
hyphy-src/src/gui/res/GTKResources/6004.png
hyphy-src/src/gui/res/GTKResources/6005.png
hyphy-src/src/gui/res/GTKResources/6006.png
hyphy-src/src/gui/res/GTKResources/6007.png
hyphy-src/src/gui/res/GTKResources/6008.png
hyphy-src/src/gui/res/GTKResources/6009.png
hyphy-src/src/gui/res/GTKResources/6010.png
hyphy-src/src/gui/res/GTKResources/6011.png
hyphy-src/src/gui/res/GTKResources/6012.png
hyphy-src/src/gui/res/GTKResources/6013.png
hyphy-src/src/gui/res/GTKResources/6014.png
hyphy-src/src/gui/res/GTKResources/6016.png
hyphy-src/src/gui/res/GTKResources/6017.png
hyphy-src/src/gui/res/GTKResources/6018.png
hyphy-src/src/gui/res/GTKResources/6019.png
hyphy-src/src/gui/res/GTKResources/6020.png
hyphy-src/src/gui/res/GTKResources/6021.png
hyphy-src/src/gui/res/GTKResources/6022.png
hyphy-src/src/gui/res/GTKResources/6030.png
hyphy-src/src/gui/res/GTKResources/6031.png
hyphy-src/src/gui/res/GTKResources/6032.png
hyphy-src/src/gui/res/GTKResources/6033.png
hyphy-src/src/gui/res/GTKResources/6034.png
hyphy-src/src/gui/res/GTKResources/6035.png
hyphy-src/src/gui/res/GTKResources/6036.png
hyphy-src/src/gui/res/GTKResources/6040.png
hyphy-src/src/gui/res/GTKResources/6041.png
hyphy-src/src/gui/res/GTKResources/6042.png
hyphy-src/src/gui/res/GTKResources/7000.png
hyphy-src/src/gui/res/GTKResources/7001.png
hyphy-src/src/gui/res/GTKResources/7002.png
hyphy-src/src/gui/res/GTKResources/7003.png
hyphy-src/src/gui/res/GTKResources/7004.png
hyphy-src/src/gui/res/GTKResources/7005.png
hyphy-src/src/gui/res/GTKResources/7010.png
hyphy-src/src/gui/res/GTKResources/7011.png
hyphy-src/src/gui/res/GTKResources/7012.png
hyphy-src/src/gui/res/GTKResources/7013.png
hyphy-src/src/gui/res/GTKResources/7014.png
hyphy-src/src/gui/res/GTKResources/7020.png
hyphy-src/src/gui/res/GTKResources/7050.png
hyphy-src/src/gui/res/GTKResources/striped.xpm
hyphy-src/src/gui/res/GTKResources/theme/.gtkrc.swp
hyphy-src/src/gui/res/GTKResources/theme/arrow_down1.png
hyphy-src/src/gui/res/GTKResources/theme/arrow_down2.png
hyphy-src/src/gui/res/GTKResources/theme/arrow_down3.png
hyphy-src/src/gui/res/GTKResources/theme/arrow_left1.png
hyphy-src/src/gui/res/GTKResources/theme/arrow_left2.png
hyphy-src/src/gui/res/GTKResources/theme/arrow_left3.png
hyphy-src/src/gui/res/GTKResources/theme/arrow_right1.png
hyphy-src/src/gui/res/GTKResources/theme/arrow_right2.png
hyphy-src/src/gui/res/GTKResources/theme/arrow_right3.png
hyphy-src/src/gui/res/GTKResources/theme/arrow_up1.png
hyphy-src/src/gui/res/GTKResources/theme/arrow_up2.png
hyphy-src/src/gui/res/GTKResources/theme/arrow_up3.png
hyphy-src/src/gui/res/GTKResources/theme/background.png
hyphy-src/src/gui/res/GTKResources/theme/blank.png
hyphy-src/src/gui/res/GTKResources/theme/button0.png
hyphy-src/src/gui/res/GTKResources/theme/button1.png
hyphy-src/src/gui/res/GTKResources/theme/button11.png
hyphy-src/src/gui/res/GTKResources/theme/button11alpha.png
hyphy-src/src/gui/res/GTKResources/theme/button12.png
hyphy-src/src/gui/res/GTKResources/theme/button12alpha.png
hyphy-src/src/gui/res/GTKResources/theme/button13.png
hyphy-src/src/gui/res/GTKResources/theme/button13alpha.png
hyphy-src/src/gui/res/GTKResources/theme/button2.png
hyphy-src/src/gui/res/GTKResources/theme/button3.png
hyphy-src/src/gui/res/GTKResources/theme/button4.png
hyphy-src/src/gui/res/GTKResources/theme/button5.png
hyphy-src/src/gui/res/GTKResources/theme/button6.png
hyphy-src/src/gui/res/GTKResources/theme/button7.png
hyphy-src/src/gui/res/GTKResources/theme/button8.png
hyphy-src/src/gui/res/GTKResources/theme/button9.png
hyphy-src/src/gui/res/GTKResources/theme/check1.png
hyphy-src/src/gui/res/GTKResources/theme/check2.png
hyphy-src/src/gui/res/GTKResources/theme/empty.png
hyphy-src/src/gui/res/GTKResources/theme/entry1.png
hyphy-src/src/gui/res/GTKResources/theme/entry2.png
hyphy-src/src/gui/res/GTKResources/theme/focus.png
hyphy-src/src/gui/res/GTKResources/theme/frame1.png
hyphy-src/src/gui/res/GTKResources/theme/frame2.png
hyphy-src/src/gui/res/GTKResources/theme/frame_gap.png
hyphy-src/src/gui/res/GTKResources/theme/frame_gap_top_end.png
hyphy-src/src/gui/res/GTKResources/theme/frame_gap_top_start.png
hyphy-src/src/gui/res/GTKResources/theme/gap_bottom.png
hyphy-src/src/gui/res/GTKResources/theme/gap_bottom_end.png
hyphy-src/src/gui/res/GTKResources/theme/gap_bottom_start.png
hyphy-src/src/gui/res/GTKResources/theme/gap_left.png
hyphy-src/src/gui/res/GTKResources/theme/gap_left_end.png
hyphy-src/src/gui/res/GTKResources/theme/gap_left_start.png
hyphy-src/src/gui/res/GTKResources/theme/gap_right.png
hyphy-src/src/gui/res/GTKResources/theme/gap_right_end.png
hyphy-src/src/gui/res/GTKResources/theme/gap_right_start.png
hyphy-src/src/gui/res/GTKResources/theme/gap_top.png
hyphy-src/src/gui/res/GTKResources/theme/gap_top_end.png
hyphy-src/src/gui/res/GTKResources/theme/gap_top_start.png
hyphy-src/src/gui/res/GTKResources/theme/handle_vert_thumb.png
hyphy-src/src/gui/res/GTKResources/theme/hline.png
hyphy-src/src/gui/res/GTKResources/theme/htrough.png
hyphy-src/src/gui/res/GTKResources/theme/menu_selected.png
hyphy-src/src/gui/res/GTKResources/theme/menu_shadow.png
hyphy-src/src/gui/res/GTKResources/theme/menubar.png
hyphy-src/src/gui/res/GTKResources/theme/notebook1.png
hyphy-src/src/gui/res/GTKResources/theme/notebook2.png
hyphy-src/src/gui/res/GTKResources/theme/notebook3.png
hyphy-src/src/gui/res/GTKResources/theme/notebook4.png
hyphy-src/src/gui/res/GTKResources/theme/notebook5.png
hyphy-src/src/gui/res/GTKResources/theme/notebook_border.png
hyphy-src/src/gui/res/GTKResources/theme/option1.png
hyphy-src/src/gui/res/GTKResources/theme/option2.png
hyphy-src/src/gui/res/GTKResources/theme/option_menu.png
hyphy-src/src/gui/res/GTKResources/theme/scrollbar_horiz1.png
hyphy-src/src/gui/res/GTKResources/theme/scrollbar_horiz2.png
hyphy-src/src/gui/res/GTKResources/theme/scrollbar_vert1.png
hyphy-src/src/gui/res/GTKResources/theme/shadow1.png
hyphy-src/src/gui/res/GTKResources/theme/shadow2.png
hyphy-src/src/gui/res/GTKResources/theme/slider_horiz1.png
hyphy-src/src/gui/res/GTKResources/theme/slider_hth1.png
hyphy-src/src/gui/res/GTKResources/theme/slider_hth2.png
hyphy-src/src/gui/res/GTKResources/theme/slider_vert1.png
hyphy-src/src/gui/res/GTKResources/theme/slider_vth1.png
hyphy-src/src/gui/res/GTKResources/theme/slider_vth2.png
hyphy-src/src/gui/res/GTKResources/theme/theme.rc
hyphy-src/src/gui/res/GTKResources/theme/vline.png
hyphy-src/src/gui/res/GTKResources/theme/vtrough.png
hyphy-src/src/gui/res/GTKResources/theme/white.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/abutton.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/abutton1.1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/abutton1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/abutton2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/abutton3.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/active1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/arrow_down.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/arrow_down1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/arrow_left.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/arrow_right.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/arrow_sub.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/arrow_up.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/base-2.0.xcf
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/base-panther1.xcf
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/base.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/base.xcf
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/base2.xcf
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/base3.xcf
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/bc.xpm
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/bg.xpm
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/bg1.xpm
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/bg2.xpm
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/blue.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/button1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/button2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/button3.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/button4.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/check-radio.xcf
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/check1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/check2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/clear.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/color.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/default.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/entry1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/ext1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/ext2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/extbottom1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/extbottom2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/extleft1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/extleft2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/extright1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/extright2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/exttop1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/exttop2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/flat.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/gem.xcf
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/green.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/handle.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/hline.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/hscroll1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/hscroll2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/hslide.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/hslide1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/hslide2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/hstrough.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/htrough.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/in.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/insen.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/lineh.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/menu-base.xcf
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/menu-item.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/menu.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/minus.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/minus1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/minus2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/normal1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/note.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/obutton1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/obutton2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/option1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/option2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/option_menu.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/option_menu2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/paned1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/paned2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/pase-panther1
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/plus.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/plus1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/plus2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/radio1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/radio2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/red.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/scroll-base.xcf
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/scroll.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/scroll1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/scroll2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/scroll3.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/scroll4.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/sdown.1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/sdown1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/sdown2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/sdown3.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/sleft1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/sleft2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/sleft3.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/slide.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/slider1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/slider2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/small-base.xcf
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/spin1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/spin2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/spin3.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/sright1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/sright2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/sright3.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/sup.1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/sup2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/sup3.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/trough.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/up.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/vscroll1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/vscroll2.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/vslide.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/vslide1.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/vstrough.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/vtrough.png
hyphy-src/src/gui/res/GTKResources/theme/.xvpics/yellow.png
hyphy-src/src/gui/res/Windows/128.cur
hyphy-src/src/gui/res/Windows/129.cur
hyphy-src/src/gui/res/Windows/130.bmp
hyphy-src/src/gui/res/Windows/131.bmp
hyphy-src/src/gui/res/Windows/132.bmp
hyphy-src/src/gui/res/Windows/132.cur
hyphy-src/src/gui/res/Windows/133.bmp
hyphy-src/src/gui/res/Windows/3000.bmp
hyphy-src/src/gui/res/Windows/333.bmp
hyphy-src/src/gui/res/Windows/400.bmp
hyphy-src/src/gui/res/Windows/4000.bmp
hyphy-src/src/gui/res/Windows/4001.bmp
hyphy-src/src/gui/res/Windows/4002.bmp
hyphy-src/src/gui/res/Windows/4003.bmp
hyphy-src/src/gui/res/Windows/401.bmp
hyphy-src/src/gui/res/Windows/4011.bmp
hyphy-src/src/gui/res/Windows/402.bmp
hyphy-src/src/gui/res/Windows/4020.bmp
hyphy-src/src/gui/res/Windows/5000.bmp
hyphy-src/src/gui/res/Windows/5001.bmp
hyphy-src/src/gui/res/Windows/5002.bmp
hyphy-src/src/gui/res/Windows/5003.bmp
hyphy-src/src/gui/res/Windows/5004.bmp
hyphy-src/src/gui/res/Windows/5005.bmp
hyphy-src/src/gui/res/Windows/5006.bmp
hyphy-src/src/gui/res/Windows/5007.bmp
hyphy-src/src/gui/res/Windows/6000.bmp
hyphy-src/src/gui/res/Windows/6001.bmp
hyphy-src/src/gui/res/Windows/6002.bmp
hyphy-src/src/gui/res/Windows/6003.bmp
hyphy-src/src/gui/res/Windows/6004.bmp
hyphy-src/src/gui/res/Windows/6005.bmp
hyphy-src/src/gui/res/Windows/6006.bmp
hyphy-src/src/gui/res/Windows/6007.bmp
hyphy-src/src/gui/res/Windows/6008.bmp
hyphy-src/src/gui/res/Windows/6009.bmp
hyphy-src/src/gui/res/Windows/6010.bmp
hyphy-src/src/gui/res/Windows/6011.bmp
hyphy-src/src/gui/res/Windows/6012.bmp
hyphy-src/src/gui/res/Windows/6013.bmp
hyphy-src/src/gui/res/Windows/6014.bmp
hyphy-src/src/gui/res/Windows/6016.bmp
hyphy-src/src/gui/res/Windows/6017.bmp
hyphy-src/src/gui/res/Windows/6018.bmp
hyphy-src/src/gui/res/Windows/6019.bmp
hyphy-src/src/gui/res/Windows/6020.bmp
hyphy-src/src/gui/res/Windows/6021.bmp
hyphy-src/src/gui/res/Windows/6022.bmp
hyphy-src/src/gui/res/Windows/6030.bmp
hyphy-src/src/gui/res/Windows/6031.bmp
hyphy-src/src/gui/res/Windows/6032.bmp
hyphy-src/src/gui/res/Windows/6033.bmp
hyphy-src/src/gui/res/Windows/6034.bmp
hyphy-src/src/gui/res/Windows/6035.bmp
hyphy-src/src/gui/res/Windows/6036.bmp
hyphy-src/src/gui/res/Windows/6040.bmp
hyphy-src/src/gui/res/Windows/6041.bmp
hyphy-src/src/gui/res/Windows/6042.bmp
hyphy-src/src/gui/res/Windows/7000.bmp
hyphy-src/src/gui/res/Windows/7001.bmp
hyphy-src/src/gui/res/Windows/7002.bmp
hyphy-src/src/gui/res/Windows/7003.bmp
hyphy-src/src/gui/res/Windows/7004.bmp
hyphy-src/src/gui/res/Windows/7005.bmp
hyphy-src/src/gui/res/Windows/7010.bmp
hyphy-src/src/gui/res/Windows/7011.bmp
hyphy-src/src/gui/res/Windows/7012.bmp
hyphy-src/src/gui/res/Windows/7013.bmp
hyphy-src/src/gui/res/Windows/7014.bmp
hyphy-src/src/gui/res/Windows/7020.bmp
hyphy-src/src/gui/res/Windows/7050.bmp
hyphy-src/src/gui/res/Windows/Win.rc
hyphy-src/src/gui/res/Windows/desk.ico
hyphy-src/src/gui/res/Windows/hyphy.bmp
hyphy-src/src/gui/res/Windows/pthreadGC2.dll
hyphy-src/src/gui/res/Windows/pthreadVC2.dll
hyphy-src/src/gui/win/HYPlatformComponent.cpp
hyphy-src/src/gui/win/HYPlatformGraphicPane.cpp
hyphy-src/src/gui/win/HYPlatformWindow.cpp
hyphy-src/src/gui/win/HYPlatfromUtils.cpp
hyphy-src/src/gui/win/Components/HYPlatformButton.cpp
hyphy-src/src/gui/win/Components/HYPlatformButtonBar.cpp
hyphy-src/src/gui/win/Components/HYPlatformCheckBox.cpp
hyphy-src/src/gui/win/Components/HYPlatformLabel.cpp
hyphy-src/src/gui/win/Components/HYPlatformPullDown.cpp
hyphy-src/src/gui/win/Components/HYPlatformSequencePane.cpp
hyphy-src/src/gui/win/Components/HYPlatformTable.cpp
hyphy-src/src/gui/win/Components/HYPlatformTextBox.cpp
hyphy-src/src/gui/win/WindowClasses/HYPlatformBootsrapWindow.cpp
hyphy-src/src/gui/win/WindowClasses/HYPlatformChartWindow.cpp
hyphy-src/src/gui/win/WindowClasses/HYPlatformConsoleWindow.cpp
hyphy-src/src/gui/win/WindowClasses/HYPlatformDBWindow.cpp
hyphy-src/src/gui/win/WindowClasses/HYPlatformDataPanel.cpp
hyphy-src/src/gui/win/WindowClasses/HYPlatformGWindow.cpp
hyphy-src/src/gui/win/WindowClasses/HYPlatformModelWindow.cpp
hyphy-src/src/gui/win/WindowClasses/HYPlatformPWindow.cpp
hyphy-src/src/gui/win/WindowClasses/HYPlatformParameterTable.cpp
hyphy-src/src/gui/win/WindowClasses/HYPlatformTWindow.cpp
hyphy-src/src/gui/win/WindowClasses/HYPlatformTreePanel.cpp
hyphy-src/src/gui/win/include/HYPlatformButtonMenu.h
hyphy-src/src/gui/win/include/HYPlatformComponent.h
hyphy-src/src/gui/win/include/HYPlatformGraphicPane.h
hyphy-src/src/gui/win/include/HYPlatformWindow.h
hyphy-src/src/gui/win/include/pthread.h
hyphy-src/src/gui/win/include/sched.h
hyphy-src/src/gui/win/include/semaphore.h
hyphy-src/src/gui/win/include/Components/HYPlatformButton.h
hyphy-src/src/gui/win/include/Components/HYPlatformButtonBar.h
hyphy-src/src/gui/win/include/Components/HYPlatformCheckbox.h
hyphy-src/src/gui/win/include/Components/HYPlatformLabel.h
hyphy-src/src/gui/win/include/Components/HYPlatformPullDown.h
hyphy-src/src/gui/win/include/Components/HYPlatformTable.h
hyphy-src/src/gui/win/include/Components/HYPlatformTextbox.h
hyphy-src/src/lib/README
hyphy-src/src/lib/batchfiles.list
hyphy-src/src/lib/build.sh
hyphy-src/src/lib/setup.py
hyphy-src/src/lib/Examples/HBL/F81.bf
hyphy-src/src/lib/Examples/HBL/HKY85.bf
hyphy-src/src/lib/Examples/HBL/data/hiv.nuc
hyphy-src/src/lib/Examples/Python/BasicHyPhy.py
hyphy-src/src/lib/Examples/R/BasicHyPhy.R
hyphy-src/src/lib/LibraryModules/Python/HyPhy/__init__.py
hyphy-src/src/lib/LibraryModules/R/HyPhy.R
hyphy-src/src/lib/Link/THyPhy.cpp
hyphy-src/src/lib/Link/THyPhy.h
hyphy-src/src/lib/SWIGWrappers/THyPhy_R.cpp
hyphy-src/src/lib/SWIGWrappers/THyPhy_py3.cpp
hyphy-src/src/lib/SWIGWrappers/THyPhy_python.cpp
hyphy-src/src/mains/gtk.cpp
hyphy-src/src/mains/mac.cpp
hyphy-src/src/mains/unix.cpp
hyphy-src/src/mains/win.cpp
hyphy-src/src/new/bayesgraph.cpp
hyphy-src/src/new/bayesgraph2.cpp
hyphy-src/src/new/bgm.cpp
hyphy-src/src/new/bgm2.cpp
hyphy-src/src/new/scfg.cpp
hyphy-src/src/new/include/bayesgraph.h
hyphy-src/src/new/include/bgm.h
hyphy-src/src/new/include/scfg.h
hyphy-src/src/ocl/opencl_kernels.cl
hyphy-src/src/utils/hyphyunixutils.cpp
hyphy-src/tests/gtests/ut_avllists.cpp
hyphy-src/tests/gtests/ut_avllists.h
hyphy-src/tests/gtests/ut_list.cpp
hyphy-src/tests/gtests/ut_lists.h
hyphy-src/tests/gtests/ut_simplelists.cpp
hyphy-src/tests/gtests/ut_simplelists.h
hyphy-src/tests/gtests/ut_strings.cpp
hyphy-src/tests/gtests/ut_strings.h
hyphy-src/tests/hbltests/Ancestors/CodonAncestors.bf
hyphy-src/tests/hbltests/Ancestors/LeafProbs.bf
hyphy-src/tests/hbltests/Ancestors/NucAncestors.bf
hyphy-src/tests/hbltests/Ancestors/NucRVAncestors.bf
hyphy-src/tests/hbltests/BFFeatures/Level1.bf
hyphy-src/tests/hbltests/BFFeatures/TreeSplits.bf
hyphy-src/tests/hbltests/BFFeatures/kernel.dump
hyphy-src/tests/hbltests/BFFeatures/Level2/File1.bf
hyphy-src/tests/hbltests/BFFeatures/Level2/File2.bf
hyphy-src/tests/hbltests/BayesianGraphicalModels/TestBGM.bf
hyphy-src/tests/hbltests/BayesianGraphicalModels/alarm.xml
hyphy-src/tests/hbltests/HMM/RateHMM.bf
hyphy-src/tests/hbltests/HMM/SmallNuc.bf
hyphy-src/tests/hbltests/HMM/SmallNucRel.bf
hyphy-src/tests/hbltests/HMM/TreeHMM.bf
hyphy-src/tests/hbltests/REL/BS-REL.bf
hyphy-src/tests/hbltests/REL/GTR_G_I.bf
hyphy-src/tests/hbltests/REL/IntermediateNucRel.bf
hyphy-src/tests/hbltests/REL/ModelMixture.bf
hyphy-src/tests/hbltests/REL/MultiplePartitions.bf
hyphy-src/tests/hbltests/REL/NY.bf
hyphy-src/tests/hbltests/REL/SmallNucRel.bf
hyphy-src/tests/hbltests/RegressionTesting/ClearConstraintsBug.bf
hyphy-src/tests/hbltests/RegressionTesting/LocalReferenceBug.bf
hyphy-src/tests/hbltests/RegressionTesting/ParseNexus.bf
hyphy-src/tests/hbltests/RegressionTesting/expModelCrash.bf
hyphy-src/tests/hbltests/RegressionTesting/unaryMinus.bf
hyphy-src/tests/hbltests/RegressionTesting/RELAX/segfault.nex
hyphy-src/tests/hbltests/RegressionTesting/RELAX/segfault.nex.RELAX.json
hyphy-src/tests/hbltests/RegressionTesting/RELAX/segfault.nex.alternative.fit
hyphy-src/tests/hbltests/RegressionTesting/RELAX/segfault.nex.partitioned_descriptive.fit
hyphy-src/tests/hbltests/RegressionTesting/RELAX/segfault.nex.tre
hyphy-src/tests/hbltests/RegressionTesting/RELAX/wrapper.bf
hyphy-src/tests/hbltests/RegressionTesting/res/69genes.test.nex
hyphy-src/tests/hbltests/Shared/REL_utils.bf
hyphy-src/tests/hbltests/Shared/TestInstrumentation.bf
hyphy-src/tests/hbltests/SimpleOptimizations/IntermediateCodon.bf
hyphy-src/tests/hbltests/SimpleOptimizations/IntermediateNuc.bf
hyphy-src/tests/hbltests/SimpleOptimizations/IntermediateProtein.bf
hyphy-src/tests/hbltests/SimpleOptimizations/LargeNuc.bf
hyphy-src/tests/hbltests/SimpleOptimizations/SmallCodon.bf
hyphy-src/tests/hbltests/SimpleOptimizations/SmallCodonLocal.bf
hyphy-src/tests/hbltests/SimpleOptimizations/TwoSequenceTest.bf
hyphy-src/tests/hbltests/SpecializedOptimizations/SingleSiteTemplate.bf
hyphy-src/tests/hbltests/SpecializedOptimizations/SiteLikelihood.bf
hyphy-src/tests/hbltests/Trickier/NonReversibleWithDynamicFrequencies.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/AllCommands.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/BranchLength.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/DeleteObject.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/Differentiate.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/DoSQL.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/Export.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/GetDataInfo.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/GetString.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/GetURL.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/HarvestFrequencies.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/JSON.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/RequireVersion.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/TestTools.ibf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/Type.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/res/test_likefunc.nex
hyphy-src/tests/hbltests/UnitTests/HBLCommands/res/test_likefunc2.nex
hyphy-src/tests/hbltests/UnitTests/HBLCommands/res/SCFG/SCFG.ibf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/res/SCFG/scfgG6c.bf
hyphy-src/tests/hbltests/UnitTests/HBLCommands/res/SCFG/small.txt
hyphy-src/tests/hbltests/UnitTests/HBLCommands/testdata/Chinook_Sqlite.sqlite
hyphy-src/tests/hbltests/UnitTests/HBLCommands/tmp/GetURL.txt
hyphy-src/tests/hbltests/data/2.fas
hyphy-src/tests/hbltests/data/2.prot
hyphy-src/tests/hbltests/data/2.tree
hyphy-src/tests/hbltests/data/5.fas
hyphy-src/tests/hbltests/data/CD2.nex
hyphy-src/tests/hbltests/data/HIVenvSweden.seq
hyphy-src/tests/hbltests/data/HMM2_synthetic.fas
hyphy-src/tests/hbltests/data/HMM4_synthetic.fas
hyphy-src/tests/hbltests/data/fluHA.nex
hyphy-src/tests/hbltests/data/fluHA_codon.nex
hyphy-src/tests/hbltests/data/mtDNA.fas
hyphy_python.egg-info/PKG-INFO
hyphy_python.egg-info/SOURCES.txt
hyphy_python.egg-info/dependency_links.txt
hyphy_python.egg-info/top_level.txt