LICENSE
MANIFEST.in
pyproject.toml
readme.md
aksha/__init__.py
aksha/_launcher.py
aksha/gpu_profile_cache.py
aksha/hmm_databases.json
aksha/initialize.py
aksha/jackhmmer.py
aksha/main.py
aksha/nucsearch.py
aksha/phmmer.py
aksha/rp16.py
aksha/scan.py
aksha/search.py
aksha.egg-info/PKG-INFO
aksha.egg-info/SOURCES.txt
aksha.egg-info/dependency_links.txt
aksha.egg-info/entry_points.txt
aksha.egg-info/requires.txt
aksha.egg-info/top_level.txt
docs/database-setup.md
native/README.md
native/cpu/avx512_tail.h
native/cpu/forward4_avx512.cpp
native/cuda/README.md
native/cuda/backward_domain_cuda.cu
native/cuda/backward_domain_cuda.h
native/cuda/bias_cuda.cu
native/cuda/bias_cuda.h
native/cuda/continuation_journal.h
native/cuda/domain_rescore_cuda.cu
native/cuda/domain_rescore_cuda.h
native/cuda/f3_threshold.cc
native/cuda/f3_threshold.h
native/cuda/forward_cuda.cu
native/cuda/forward_cuda.h
native/cuda/postfilter_cuda.cu
native/cuda/postfilter_cuda.h
native/cuda/ssv_cuda.cu
native/cuda/ssv_cuda.h
native/patches/pyhmmer-0.12.0-avx512-tail.patch
native/patches/pyhmmer-0.12.0-compact-domains.patch
native/patches/pyhmmer-0.12.0-intrarow-release.patch
native/patches/pyhmmer-0.12.0-plan7gpu.patch
native/patches/pyhmmer-0.12.0-simple-regions.patch
native/python/plan7_gpu/__init__.py
native/python/plan7_gpu/_abi.py
native/python/plan7_gpu/_fingerprint.py
native/python/plan7_gpu/_mandatory_seed.py
native/python/plan7_gpu/_native.pyx
native/python/plan7_gpu/_pipeline.pyx
native/python/plan7_gpu/_private_tuning.py
native/python/plan7_gpu/_telemetry.py
native/python/plan7_gpu/adapter.py
native/python/plan7_gpu/astra_search.py
native/python/plan7_gpu/pressed_manifest.py
native/python/plan7_gpu/telemetry_report.py
release/BUILD.md
release/INSTALL.md
release/PUBLISH.md
release/THIRD_PARTY_NOTICES.md
release/build-requirements.txt
release/build.py
release/bundle.py
release/install_smoke.py
release/migrate_sources.py
release/prepare.py
release/runtime-pyproject.toml.in
release/scheduler_fix_bundle.py
release/source-lock.json
release/source-migration.json
tests/__init__.py
tests/test_continuation_format.py
tests/test_cpu_allocator_launcher.py
tests/test_cpu_stream_profiles.py
tests/test_gpu_profile_cache.py
tests/test_gpu_search.py