├── .github └── workflows │ ├── cmake.yml │ ├── codeql-analysis.yml │ ├── python.yml │ └── wheels.yml ├── .gitignore ├── .gitmodules ├── AUTHORS ├── CLAUDE.md ├── CMakeLists.txt ├── CONTRIBUTING.md ├── COPYING ├── ChangeLog ├── README-python.md ├── README.md ├── doc ├── images │ ├── Balibase_scores.jpeg │ ├── Balibase_scores.png │ ├── Bralibase_scores.jpeg │ ├── Homfam_scores.jpeg │ └── Quantest2_scores.jpeg └── paper │ ├── kalign3.bib │ ├── kalign3.org │ └── revision │ └── main.tex ├── lib ├── CMakeLists.txt ├── include │ └── kalign │ │ └── kalign.h ├── kalignConfig.cmake.in └── src │ ├── aln_controller.c │ ├── aln_controller.h │ ├── aln_mem.c │ ├── aln_mem.h │ ├── aln_param.c │ ├── aln_param.h │ ├── aln_profileprofile.c │ ├── aln_profileprofile.h │ ├── aln_run.c │ ├── aln_run.h │ ├── aln_seqprofile.c │ ├── aln_seqprofile.h │ ├── aln_seqseq.c │ ├── aln_seqseq.h │ ├── aln_setup.c │ ├── aln_setup.h │ ├── aln_struct.h │ ├── aln_wrap.c │ ├── aln_wrap.h │ ├── alphabet.c │ ├── alphabet.h │ ├── bisectingKmeans.c │ ├── bisectingKmeans.h │ ├── bpm.c │ ├── bpm.h │ ├── bpm_test.c │ ├── core.h │ ├── coretralign.c │ ├── coretralign.h │ ├── esl_stopwatch.c │ ├── esl_stopwatch.h │ ├── euclidean_dist.c │ ├── euclidean_dist.h │ ├── io.h │ ├── mod_tldevel.h │ ├── msa_alloc.c │ ├── msa_alloc.h │ ├── msa_check.c │ ├── msa_check.h │ ├── msa_cmp.c │ ├── msa_cmp.h │ ├── msa_io.c │ ├── msa_io.h │ ├── msa_misc.c │ ├── msa_misc.h │ ├── msa_op.c │ ├── msa_op.h │ ├── msa_sort.c │ ├── msa_sort.h │ ├── msa_struct.h │ ├── pick_anchor.c │ ├── pick_anchor.h │ ├── sequence_distance.c │ ├── sequence_distance.h │ ├── task.c │ ├── task.h │ ├── test.c │ ├── test.h │ ├── tldevel.c │ ├── tldevel.h │ ├── tlmisc.c │ ├── tlmisc.h │ ├── tlrng.c │ ├── tlrng.h │ ├── version.h.in │ ├── weave_alignment.c │ └── weave_alignment.h ├── pyproject.toml ├── pytest.ini ├── python-docs ├── python-api.md ├── python-ecosystem.md ├── python-performance.md ├── python-quickstart.md └── python-troubleshooting.md ├── python-examples ├── README.md ├── basic_usage.py ├── ecosystem_integration.py ├── performance_benchmarks.py └── sample_sequences.fasta ├── python-kalign ├── __init__.py ├── _core.cpp ├── cli.py ├── io.py ├── py.typed └── utils.py ├── scripts ├── balibase_test.org ├── benchmark.org └── bralibase.org ├── src ├── CMakeLists.txt ├── parameters.c ├── parameters.h ├── run_kalign.c ├── run_reformat.c └── version.h.in ├── test_thresholds.py ├── tests ├── CMakeLists.txt ├── data │ ├── BB11001.msf │ ├── BB11001.tfa │ ├── BB11001_EOF.msf │ ├── BB12006.msf │ ├── BB12006.tfa │ ├── BB30014.msf │ ├── BB30014.tfa │ ├── README │ ├── a2m.good.1 │ ├── a2m.good.2 │ ├── afa.good.1 │ ├── afa.good.2 │ ├── afa.good.3 │ ├── clustal.good.1 │ ├── clustal.good.2 │ ├── small.fa │ ├── tiny.fa │ └── tiny_internal.fa ├── dssim.c ├── dssim.h ├── dssim_test.c ├── kalign_cmp_test.c ├── kalign_io_test.c ├── kalign_lib_test.c ├── kalign_lib_testCXX.cpp ├── large_benchmark.c ├── python │ ├── conftest.py │ ├── pytest.ini │ ├── test_basic_alignment.py │ ├── test_data │ │ ├── dna_sequences.fasta │ │ ├── invalid_sequences.fasta │ │ ├── protein_sequences.fasta │ │ └── rna_sequences.fasta │ ├── test_ecosystem_integration.py │ ├── test_edge_cases.py │ ├── test_error_handling.py │ ├── test_file_operations.py │ ├── test_input_validation.py │ ├── test_integration.py │ ├── test_parameters.py │ ├── test_performance.py │ ├── test_sequence_types.py │ └── test_thresholds.py └── zig_test.c └── uv.lock /.github/workflows/cmake.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TimoLassmann/kalign/HEAD/.github/workflows/cmake.yml -------------------------------------------------------------------------------- /.github/workflows/codeql-analysis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TimoLassmann/kalign/HEAD/.github/workflows/codeql-analysis.yml 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