LICENSE.md
MANIFEST.in
README.rst
README_PYPI.md
pyproject.toml
setup.cfg
setup.py
sonicparanoid/__init__.py
sonicparanoid/archiver.pyx
sonicparanoid/archortho.py
sonicparanoid/d2v.pyx
sonicparanoid/dev-sonic_infer_ortho_table.py
sonicparanoid/domortho.pyx
sonicparanoid/essentials_c.pyx
sonicparanoid/extract_results.py
sonicparanoid/get_pfam_profiles.py
sonicparanoid/get_test_data.py
sonicparanoid/graph_c.pyx
sonicparanoid/hdr_mapping.py
sonicparanoid/inpyranoid.py
sonicparanoid/inpyranoid_c.pyx
sonicparanoid/mcl_c.pyx
sonicparanoid/mmseqs_parser_c.pyx
sonicparanoid/ortho_merger.pyx
sonicparanoid/orthogroups.py
sonicparanoid/ortholog_detection.py
sonicparanoid/process_output.py
sonicparanoid/profile_search.pyx
sonicparanoid/remap_tables_c.pyx
sonicparanoid/seq_tools.py
sonicparanoid/sonic_paranoid.py
sonicparanoid/sonic_paranoid_extract.py
sonicparanoid/sys_tools.py
sonicparanoid/test-dev-compare-and-merge-predicted-pairs.py
sonicparanoid/test-dev-create-corpus-from-raw-profile-searches.py
sonicparanoid/test-dev-create-corpus.py
sonicparanoid/test-dev-create_pfam_profile_db.py
sonicparanoid/test-dev-extract-archs-from-raw-profile-searches.py
sonicparanoid/test-dev-extract-documents-from-raw-archs.py
sonicparanoid/test-dev-grid-search.py
sonicparanoid/test-dev-infer-domain-orthologs.py
sonicparanoid/test-dev-infer-ortholog-archs-from-profile-searches.py
sonicparanoid/test-dev-merge-arch-and-graph-based-orthologs.py
sonicparanoid/test-dev-profile_search.py
sonicparanoid/test-dev-remap-ortholog-pairs.py
sonicparanoid/workers.py
sonicparanoid.egg-info/PKG-INFO
sonicparanoid.egg-info/SOURCES.txt
sonicparanoid.egg-info/dependency_links.txt
sonicparanoid.egg-info/entry_points.txt
sonicparanoid.egg-info/not-zip-safe
sonicparanoid.egg-info/requires.txt
sonicparanoid.egg-info/top_level.txt
sonicparanoid/bin/README.md
sonicparanoid/example/test_input/chlamydia_trachomatis
sonicparanoid/example/test_input/deinococcus_radiodurans
sonicparanoid/example/test_input/gloeobacter_violaceus
sonicparanoid/example/test_input/thermotoga_maritima
sonicparanoid/example/test_output/README.txt
sonicparanoid/pfam_files/Pfam-A.hmm.dat.gz
sonicparanoid/pfam_files/pfam_db.info.md
sonicparanoid/pfam_files/pfama-mmseqs.tar.gz
sonicparanoid/software_packages/README.md
sonicparanoid/software_packages/blastp.xz
sonicparanoid/software_packages/diamond.xz
sonicparanoid/software_packages/makeblastdb.xz
sonicparanoid/software_packages/mcl_linux
sonicparanoid/software_packages/mmseqs_linux_avx2.xz
sonicparanoid/software_packages/mmseqs_linux_sse41.xz