set(alignment_header_files
        mmseqs/alignment/alignment.h
        mmseqs/alignment/compressedA3M.h
        mmseqs/alignment/evalueComputation.h
        mmseqs/alignment/matcher.h
        mmseqs/alignment/msaFilter.h
        mmseqs/alignment/multipleAlignment.h
        mmseqs/alignment/pSSMCalculator.h
        mmseqs/alignment/pSSMMasker.h
        mmseqs/alignment/stripedSmithWaterman.h
        mmseqs/alignment/bandedNucleotideAligner.h
        mmseqs/alignment/distanceCalculator.h
        PARENT_SCOPE
        )

set(alignment_source_files
        mmseqs/alignment/alignment.cpp
        mmseqs/alignment/compressedA3M.cpp
        mmseqs/alignment/main.cpp
        mmseqs/alignment/matcher.cpp
        mmseqs/alignment/msaFilter.cpp
        mmseqs/alignment/multipleAlignment.cpp
        mmseqs/alignment/pSSMCalculator.cpp
        mmseqs/alignment/stripedSmithWaterman.cpp
        mmseqs/alignment/bandedNucleotideAligner.cpp
        mmseqs/alignment/rescorediagonal.cpp
        PARENT_SCOPE
        )
