├── .clang-format ├── .gitignore ├── .travis.yml ├── COPYING ├── INSTALL ├── Makefile.am ├── README.md ├── andi-manual.pdf ├── configure.ac ├── docs ├── Doxyfile ├── Makefile.am ├── andi.1.in └── manual │ ├── andi-manual.tex │ ├── andi_labels.pdf │ ├── references.bib │ └── version.tex.in ├── libs ├── Makefile.am ├── pfasta.c └── pfasta.h ├── m4 └── ax_cxx_compile_stdcxx_11.m4 ├── opt ├── Makefile.am ├── compat-stdlib.h ├── compat-string.h ├── reallocarray.c └── strchrnul.c ├── scripts ├── _andi ├── failed.zsh ├── maf2phy.awk └── vmatch.sh ├── src ├── Makefile.am ├── andi.c ├── dist_hack.h ├── esa.c ├── esa.h ├── global.h ├── io.c ├── io.h ├── model.c ├── model.h ├── process.c ├── process.h ├── sequence.c └── sequence.h └── test ├── Makefile.am ├── low_homo.sh ├── nan.sh ├── test_esa.c ├── test_extra.sh ├── test_fasta.cxx ├── test_join.sh ├── test_process.c ├── test_random.sh └── test_seq.c /.clang-format: -------------------------------------------------------------------------------- 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