├── .clang-format ├── .clang-tidy ├── .gitignore ├── .gitmodules ├── .travis.yml ├── CMakeLists.txt ├── Dockerfile ├── LICENSE ├── benchmark ├── CMakeLists.txt └── src │ ├── CMakeLists.txt │ ├── main.cpp │ ├── model.cpp │ └── tree.cpp ├── docs ├── README.md └── images │ └── logo.png ├── lib ├── CMakeLists.txt └── lbfgsb │ ├── CMakeLists.txt │ ├── License.txt │ ├── lbfgsb.c │ ├── lbfgsb.h │ ├── linesearch.c │ ├── linpack.c │ ├── miniCBLAS.c │ └── subalgorithms.c ├── makefile ├── src ├── CMakeLists.txt ├── checkpoint.cpp ├── checkpoint.hpp ├── debug.h ├── main.cpp ├── model.cpp ├── model.hpp ├── msa.cpp ├── msa.hpp ├── tree.cpp ├── tree.hpp ├── util.cpp └── util.hpp └── test ├── CMakeLists.txt ├── data ├── dna │ ├── 10.fasta │ ├── 101.phy │ ├── 125.phy │ └── single.phy ├── freqs │ └── uniform.freqs └── tree │ ├── 10.tree │ ├── 101.tree │ ├── 125.tree │ ├── 140.tree │ ├── sanity_check1.tree │ ├── sanity_check2.tree │ ├── sanity_check3.tree │ └── single.tree ├── lib └── CMakeLists.txt └── 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