LICENSE
README.md
pyproject.toml
setup.py
src/pyseqalign/__init__.py
src/pyseqalign/accel.py
src/pyseqalign/core/__init__.py
src/pyseqalign/core/alignment.py
src/pyseqalign/core/needleman_wunsch.py
src/pyseqalign/core/smith_waterman.py
src/pyseqalign/cpp/build_cpp_aligner.sh
src/pyseqalign/cpp/cpp_aligner.cpp
src/pyseqalign/learning/__init__.py
src/pyseqalign/learning/aleph.py
src/pyseqalign/learning/base.py
src/pyseqalign/learning/popper.py
src/pyseqalign/learning/task_builder.py
src/pyseqalign/learning/aleph_files/__init__.py
src/pyseqalign/learning/aleph_files/aleph_swi_ak.pl
src/pyseqalign/prolog/__init__.py
src/pyseqalign/prolog/engine.py
src/pyseqalign/prolog/knowledge/__init__.py
src/pyseqalign/prolog/knowledge/amino_acids.pl
src/pyseqalign/prolog/knowledge/blosum50.pl
src/pyseqalign/prolog/knowledge/defaults.pl
src/pyseqalign/prolog/knowledge/distances.pl
src/pyseqalign/scoring/__init__.py
src/pyseqalign/scoring/distance.py
src/pyseqalign/scoring/matrices.py
src/pyseqalign/scoring/matrix_data/BLOSUM100
src/pyseqalign/scoring/matrix_data/BLOSUM50
src/pyseqalign/scoring/matrix_data/BLOSUM60
src/pyseqalign/scoring/matrix_data/BLOSUM62
src/pyseqalign/scoring/matrix_data/BLOSUM70
src/pyseqalign/scoring/matrix_data/BLOSUM80
src/pyseqalign/scoring/matrix_data/BLOSUM90
src/pyseqalign/scoring/matrix_data/PAM150
src/pyseqalign/scoring/matrix_data/PAM200
src/pyseqalign/scoring/matrix_data/PAM250
src/pyseqalign/scoring/matrix_data/PAM50
src/pyseqalign/scoring/matrix_data/__init__.py
src/pyseqalign/utils/__init__.py
src/pyseqalign/utils/helpers.py
src/pyseqalignment.egg-info/PKG-INFO
src/pyseqalignment.egg-info/SOURCES.txt
src/pyseqalignment.egg-info/dependency_links.txt
src/pyseqalignment.egg-info/requires.txt
src/pyseqalignment.egg-info/top_level.txt
tests/test_learning.py
tests/test_needleman_wunsch.py
tests/test_scoring.py
tests/test_smith_waterman.py
tests/test_utils.py