CODE_OF_CONDUCT.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
pairk/__init__.py
pairk/_version.py
pairk/examples.py
pairk/py.typed
pairk/utilities.py
pairk.egg-info/PKG-INFO
pairk.egg-info/SOURCES.txt
pairk.egg-info/dependency_links.txt
pairk.egg-info/not-zip-safe
pairk.egg-info/requires.txt
pairk.egg-info/top_level.txt
pairk/backend/__init__.py
pairk/backend/exceptions.py
pairk/backend/conservation/__init__.py
pairk/backend/conservation/kmer_conservation.py
pairk/backend/conservation/capra_singh_functions/__init__.py
pairk/backend/conservation/capra_singh_functions/capra_singh_2007_scores.py
pairk/backend/kmer_alignment/__init__.py
pairk/backend/kmer_alignment/esm_embedding_distance.py
pairk/backend/kmer_alignment/needleman_tools.py
pairk/backend/kmer_alignment/scoring_matrix.py
pairk/backend/kmer_alignment/scoring_matrix_needleman.py
pairk/backend/tools/__init__.py
pairk/backend/tools/esm_tools.py
pairk/backend/tools/matrices.py
pairk/backend/tools/pairwise_tools.py
pairk/backend/tools/plotting_tools.py
pairk/backend/tools/pssms.py
pairk/backend/tools/sequence_utils.py
pairk/data/README.md
pairk/data/__init__.py
pairk/data/example_alignment_9606_0_00294e-idraln-555_to_971-idr-440_to_665.fasta
pairk/data/matrices/BLOSUM62
pairk/data/matrices/EDSSMat50
pairk/data/matrices/__init__.py
pairk/data/matrices/grantham.csv
pairk/data/matrices/grantham_similarity_norm.csv
pairk/data/matrices/grantham_similarity_normx100_aligner_compatible
pairk/single_kmer/__init__.py
pairk/tests/__init__.py
pairk/tests/test_pairk.py