├── .gitignore ├── AUTHORS ├── COPYING ├── ChangeLog ├── Dockerfile ├── INSTALL ├── LICENSE_1_0.txt ├── Makefile.am ├── NEWS ├── README ├── README.md ├── autogen.sh ├── bump_version.bash ├── configure.ac ├── docker-compose.yml ├── m4 ├── ax_boost_base.m4 ├── ax_boost_date_time.m4 ├── ax_boost_filesystem.m4 ├── ax_boost_iostreams.m4 ├── ax_boost_program_options.m4 ├── ax_boost_regex.m4 ├── ax_boost_system.m4 ├── ax_boost_thread.m4 ├── ax_boost_timer.m4 ├── ax_boost_unit_test_framework.m4 └── ax_check_library.m4 ├── mtrx ├── BLOSUM30 ├── BLOSUM45 ├── BLOSUM62 ├── BLOSUM80 ├── GONNET250 ├── PAM120 ├── PAM20 ├── PAM350 ├── PAM60 └── mkmat_h.pl ├── rsrc ├── error.html └── index.html ├── run_test.sh ├── scripts ├── dssp2fasta.pl ├── hssp2admin.pl ├── hssp2admin.sql ├── hssp2ix.pm ├── hssp3to1.pl ├── lisa │ └── makefile ├── split-fasta.pl └── update-hssp2 ├── singularity.def ├── src ├── align-2d.h ├── blast.cpp ├── blast.h ├── buffer.h ├── fasta.cpp ├── fasta.h ├── fetchdbrefs.cpp ├── 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