Debian 12 (Bookworm) native package

python3-cogent3

framework for genomic biology

Packages / Debian 12 (Bookworm) / python / python3-cogent3

[Source: python-cogent]

Package: python3-cogent3 (2023.2.12a1+dfsg-2+deb12u1)

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [github.com]

Similar packages:

[python-cogent-doc]
docs for python3-cogent3

framework for genomic biology

Other Packages Related to python3-cogent3:

dep: [python3-chardet]
Universal Character Encoding Detector (Python3)
dep: [python3-numba]
native machine code compiler for Python 3
dep: [python3-numpy] (>= 1:1.22.0)
Fast array facility to the Python 3 language
dep: python3-numpy-abi9
Package not available
dep: [python3-scipy]
scientific tools for Python 3
dep: [python3-scitrack]
Python3 library to track scientific data
dep: [python3-tinydb]
document oriented database optimized
dep: [python3-tqdm]
fast, extensible progress bar for Python 3 and CLI tool
dep: [python3-typing-extensions]
Backported and Experimental Type Hints for Python
dep: [python3] [any]
interactive high-level object-oriented language (default python3 version)
dep: [python3-matplotlib]
Python based plotting system in a style similar to Matlab (Python 3)
dep: [python3-pandas]
data structures for "relational" or "labeled" data
dep: [python3-plotly]
Python 3 plotting library for publication-quality graphs

rec: [ncbi-blast+-legacy]
NCBI Blast legacy call script
rec: [dialign]
Segment-based multiple sequence alignment

sug: [python-cogent-doc]
docs for python3-cogent3

Download python3-cogent3

Architecture	Package Size	Installed Size	Files
amd64	1.8 MiB	6.5 MiB	[list of files]
arm64	1.8 MiB	6.5 MiB	[list of files]

Package file paths (391)

Showing the first 250 sorted package-associated paths. Use file search to locate a specific path.

/usr/lib/python3/dist-packages/cogent3-2023.2.12a1.dist-info/METADATA
/usr/lib/python3/dist-packages/cogent3-2023.2.12a1.dist-info/RECORD
/usr/lib/python3/dist-packages/cogent3-2023.2.12a1.dist-info/WHEEL
/usr/lib/python3/dist-packages/cogent3/align/align.py
/usr/lib/python3/dist-packages/cogent3/align/compare_numba.py
/usr/lib/python3/dist-packages/cogent3/align/dp_calculation.py
/usr/lib/python3/dist-packages/cogent3/align/indel_model.py
/usr/lib/python3/dist-packages/cogent3/align/indel_positions.py
/usr/lib/python3/dist-packages/cogent3/align/__init__.py
/usr/lib/python3/dist-packages/cogent3/align/pairwise_pogs_numba.py
/usr/lib/python3/dist-packages/cogent3/align/pairwise.py
/usr/lib/python3/dist-packages/cogent3/align/pairwise_seqs_numba.py
/usr/lib/python3/dist-packages/cogent3/align/progressive.py
/usr/lib/python3/dist-packages/cogent3/align/pycompare.py
/usr/lib/python3/dist-packages/cogent3/align/traceback.py
/usr/lib/python3/dist-packages/cogent3/app/align.py
/usr/lib/python3/dist-packages/cogent3/app/composable.py
/usr/lib/python3/dist-packages/cogent3/app/data_store_new.py
/usr/lib/python3/dist-packages/cogent3/app/data_store.py
/usr/lib/python3/dist-packages/cogent3/app/dist.py
/usr/lib/python3/dist-packages/cogent3/app/evo.py
/usr/lib/python3/dist-packages/cogent3/app/__init__.py
/usr/lib/python3/dist-packages/cogent3/app/io_new.py
/usr/lib/python3/dist-packages/cogent3/app/io.py
/usr/lib/python3/dist-packages/cogent3/app/result.py
/usr/lib/python3/dist-packages/cogent3/app/sample.py
/usr/lib/python3/dist-packages/cogent3/app/sqlite_data_store.py
/usr/lib/python3/dist-packages/cogent3/app/translate.py
/usr/lib/python3/dist-packages/cogent3/app/tree.py
/usr/lib/python3/dist-packages/cogent3/app/typing.py
/usr/lib/python3/dist-packages/cogent3/cluster/__init__.py
/usr/lib/python3/dist-packages/cogent3/cluster/UPGMA.py
/usr/lib/python3/dist-packages/cogent3/core/alignment.py
/usr/lib/python3/dist-packages/cogent3/core/alphabet.py
/usr/lib/python3/dist-packages/cogent3/core/annotation.py
/usr/lib/python3/dist-packages/cogent3/core/genetic_code.py
/usr/lib/python3/dist-packages/cogent3/core/info.py
/usr/lib/python3/dist-packages/cogent3/core/__init__.py
/usr/lib/python3/dist-packages/cogent3/core/location.py
/usr/lib/python3/dist-packages/cogent3/core/moltype.py
/usr/lib/python3/dist-packages/cogent3/core/profile.py
/usr/lib/python3/dist-packages/cogent3/core/sequence.py
/usr/lib/python3/dist-packages/cogent3/core/tree.py
/usr/lib/python3/dist-packages/cogent3/data/energy_params.py
/usr/lib/python3/dist-packages/cogent3/data/__init__.py
/usr/lib/python3/dist-packages/cogent3/data/molecular_weight.py
/usr/lib/python3/dist-packages/cogent3/draw/dendrogram.py
/usr/lib/python3/dist-packages/cogent3/draw/dotplot.py
/usr/lib/python3/dist-packages/cogent3/draw/drawable.py
/usr/lib/python3/dist-packages/cogent3/draw/__init__.py
/usr/lib/python3/dist-packages/cogent3/draw/letter.py
/usr/lib/python3/dist-packages/cogent3/draw/logo.py
/usr/lib/python3/dist-packages/cogent3/evolve/best_likelihood.py
/usr/lib/python3/dist-packages/cogent3/evolve/bootstrap.py
/usr/lib/python3/dist-packages/cogent3/evolve/coevolution.py
/usr/lib/python3/dist-packages/cogent3/evolve/discrete_markov.py
/usr/lib/python3/dist-packages/cogent3/evolve/distance.py
/usr/lib/python3/dist-packages/cogent3/evolve/fast_distance.py
/usr/lib/python3/dist-packages/cogent3/evolve/__init__.py
/usr/lib/python3/dist-packages/cogent3/evolve/likelihood_calculation.py
/usr/lib/python3/dist-packages/cogent3/evolve/likelihood_function.py
/usr/lib/python3/dist-packages/cogent3/evolve/likelihood_tree_numba.py
/usr/lib/python3/dist-packages/cogent3/evolve/likelihood_tree.py
/usr/lib/python3/dist-packages/cogent3/evolve/models.py
/usr/lib/python3/dist-packages/cogent3/evolve/motif_prob_model.py
/usr/lib/python3/dist-packages/cogent3/evolve/ns_substitution_model.py
/usr/lib/python3/dist-packages/cogent3/evolve/pairwise_distance_numba.py
/usr/lib/python3/dist-packages/cogent3/evolve/parameter_controller.py
/usr/lib/python3/dist-packages/cogent3/evolve/predicate.py
/usr/lib/python3/dist-packages/cogent3/evolve/simulate.py
/usr/lib/python3/dist-packages/cogent3/evolve/solved_models_numba.py
/usr/lib/python3/dist-packages/cogent3/evolve/solved_models.py
/usr/lib/python3/dist-packages/cogent3/evolve/substitution_calculation.py
/usr/lib/python3/dist-packages/cogent3/evolve/substitution_model.py
/usr/lib/python3/dist-packages/cogent3/format/alignment.py
/usr/lib/python3/dist-packages/cogent3/format/bedgraph.py
/usr/lib/python3/dist-packages/cogent3/format/clustal.py
/usr/lib/python3/dist-packages/cogent3/format/fasta.py
/usr/lib/python3/dist-packages/cogent3/format/gde.py
/usr/lib/python3/dist-packages/cogent3/format/__init__.py
/usr/lib/python3/dist-packages/cogent3/format/nexus.py
/usr/lib/python3/dist-packages/cogent3/format/paml.py
/usr/lib/python3/dist-packages/cogent3/format/phylip.py
/usr/lib/python3/dist-packages/cogent3/format/table.py
/usr/lib/python3/dist-packages/cogent3/format/util.py
/usr/lib/python3/dist-packages/cogent3/__init__.py
/usr/lib/python3/dist-packages/cogent3/maths/distance_transform.py
/usr/lib/python3/dist-packages/cogent3/maths/geometry.py
/usr/lib/python3/dist-packages/cogent3/maths/__init__.py
/usr/lib/python3/dist-packages/cogent3/maths/markov.py
/usr/lib/python3/dist-packages/cogent3/maths/matrix_exponential_integration.py
/usr/lib/python3/dist-packages/cogent3/maths/matrix_exponentiation.py
/usr/lib/python3/dist-packages/cogent3/maths/matrix_logarithm.py
/usr/lib/python3/dist-packages/cogent3/maths/measure.py
/usr/lib/python3/dist-packages/cogent3/maths/optimisers.py
/usr/lib/python3/dist-packages/cogent3/maths/period_numba.py
/usr/lib/python3/dist-packages/cogent3/maths/period.py
/usr/lib/python3/dist-packages/cogent3/maths/scipy_optimisers.py
/usr/lib/python3/dist-packages/cogent3/maths/scipy_optimize.py
/usr/lib/python3/dist-packages/cogent3/maths/simannealingoptimiser.py
/usr/lib/python3/dist-packages/cogent3/maths/solve.py
/usr/lib/python3/dist-packages/cogent3/maths/stats/contingency.py
/usr/lib/python3/dist-packages/cogent3/maths/stats/distribution.py
/usr/lib/python3/dist-packages/cogent3/maths/stats/information_criteria.py
/usr/lib/python3/dist-packages/cogent3/maths/stats/__init__.py
/usr/lib/python3/dist-packages/cogent3/maths/stats/jackknife.py
/usr/lib/python3/dist-packages/cogent3/maths/stats/kendall.py
/usr/lib/python3/dist-packages/cogent3/maths/stats/ks.py
/usr/lib/python3/dist-packages/cogent3/maths/stats/number.py
/usr/lib/python3/dist-packages/cogent3/maths/stats/period.py
/usr/lib/python3/dist-packages/cogent3/maths/stats/special.py
/usr/lib/python3/dist-packages/cogent3/maths/stats/test.py
/usr/lib/python3/dist-packages/cogent3/maths/util.py
/usr/lib/python3/dist-packages/cogent3/parse/blast.py
/usr/lib/python3/dist-packages/cogent3/parse/blast_xml.py
/usr/lib/python3/dist-packages/cogent3/parse/cigar.py
/usr/lib/python3/dist-packages/cogent3/parse/cisbp.py
/usr/lib/python3/dist-packages/cogent3/parse/clustal.py
/usr/lib/python3/dist-packages/cogent3/parse/cogent3_json.py
/usr/lib/python3/dist-packages/cogent3/parse/dialign.py
/usr/lib/python3/dist-packages/cogent3/parse/ebi.py
/usr/lib/python3/dist-packages/cogent3/parse/fasta.py
/usr/lib/python3/dist-packages/cogent3/parse/gbseq.py
/usr/lib/python3/dist-packages/cogent3/parse/gcg.py
/usr/lib/python3/dist-packages/cogent3/parse/genbank.py
/usr/lib/python3/dist-packages/cogent3/parse/gff.py
/usr/lib/python3/dist-packages/cogent3/parse/greengenes.py
/usr/lib/python3/dist-packages/cogent3/parse/__init__.py
/usr/lib/python3/dist-packages/cogent3/parse/jaspar.py
/usr/lib/python3/dist-packages/cogent3/parse/locuslink.py
/usr/lib/python3/dist-packages/cogent3/parse/ncbi_taxonomy.py
/usr/lib/python3/dist-packages/cogent3/parse/newick.py
/usr/lib/python3/dist-packages/cogent3/parse/nexus.py
/usr/lib/python3/dist-packages/cogent3/parse/paml_matrix.py
/usr/lib/python3/dist-packages/cogent3/parse/paml.py
/usr/lib/python3/dist-packages/cogent3/parse/phylip.py
/usr/lib/python3/dist-packages/cogent3/parse/psl.py
/usr/lib/python3/dist-packages/cogent3/parse/rdb.py
/usr/lib/python3/dist-packages/cogent3/parse/record_finder.py
/usr/lib/python3/dist-packages/cogent3/parse/record.py
/usr/lib/python3/dist-packages/cogent3/parse/sequence.py
/usr/lib/python3/dist-packages/cogent3/parse/table.py
/usr/lib/python3/dist-packages/cogent3/parse/tinyseq.py
/usr/lib/python3/dist-packages/cogent3/parse/tree.py
/usr/lib/python3/dist-packages/cogent3/parse/tree_xml.py
/usr/lib/python3/dist-packages/cogent3/parse/unigene.py
/usr/lib/python3/dist-packages/cogent3/phylo/consensus.py
/usr/lib/python3/dist-packages/cogent3/phylo/__init__.py
/usr/lib/python3/dist-packages/cogent3/phylo/least_squares.py
/usr/lib/python3/dist-packages/cogent3/phylo/maximum_likelihood.py
/usr/lib/python3/dist-packages/cogent3/phylo/nj.py
/usr/lib/python3/dist-packages/cogent3/phylo/tree_collection.py
/usr/lib/python3/dist-packages/cogent3/phylo/tree_space.py
/usr/lib/python3/dist-packages/cogent3/phylo/util.py
/usr/lib/python3/dist-packages/cogent3/recalculation/calculation.py
/usr/lib/python3/dist-packages/cogent3/recalculation/definition.py
/usr/lib/python3/dist-packages/cogent3/recalculation/__init__.py
/usr/lib/python3/dist-packages/cogent3/recalculation/scope.py
/usr/lib/python3/dist-packages/cogent3/recalculation/setting.py
/usr/lib/python3/dist-packages/cogent3/util/checkpointing.py
/usr/lib/python3/dist-packages/cogent3/util/deserialise.py
/usr/lib/python3/dist-packages/cogent3/util/dict_array.py
/usr/lib/python3/dist-packages/cogent3/util/__init__.py
/usr/lib/python3/dist-packages/cogent3/util/io.py
/usr/lib/python3/dist-packages/cogent3/util/misc.py
/usr/lib/python3/dist-packages/cogent3/util/parallel.py
/usr/lib/python3/dist-packages/cogent3/util/progress_display.py
/usr/lib/python3/dist-packages/cogent3/util/recode_alignment.py
/usr/lib/python3/dist-packages/cogent3/util/table.py
/usr/lib/python3/dist-packages/cogent3/util/transform.py
/usr/lib/python3/dist-packages/cogent3/util/union_dict.py
/usr/lib/python3/dist-packages/cogent3/util/warning.py
/usr/lib/python3/dist-packages/data/1A1X.pdb
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/usr/lib/python3/dist-packages/data/brca1.fasta
/usr/lib/python3/dist-packages/data/c_elegans_WS199_dna_shortened.fasta
/usr/lib/python3/dist-packages/data/c_elegans_WS199_shortened_gff.gff3
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/usr/lib/python3/dist-packages/data/ENSG00000198712.fa
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/usr/lib/python3/dist-packages/data/Homo_sapiens_codon_usage.pri
/usr/lib/python3/dist-packages/data/interleaved.phylip
/usr/lib/python3/dist-packages/data/long_testseqs.fasta
/usr/lib/python3/dist-packages/data/long_testseqs.tree
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/usr/share/doc/python3-cogent3/tests/data/c_elegans_WS199_shortened_gff.gff3
/usr/share/doc/python3-cogent3/tests/data/ensembl_sample.gff3
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/usr/share/doc/python3-cogent3/tests/data/Homo_sapiens_codon_usage.pri.gz

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

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Version	Release	Architecture	Repository	Package size	Installed size	Publisher repository artifact
2023.2.12a1+dfsg-2+deb12u1	bookworm / main	amd64	Debian 12 · main · amd64	1.8 MiB	6.5 MiB	pool/main/p/python-cogent/python3-cogent3_2023.2.12a1+dfsg-2+deb12u1_amd64.deb
2023.2.12a1+dfsg-2+deb12u1	bookworm / main	arm64	Debian 12 · main · arm64	1.8 MiB	6.5 MiB	pool/main/p/python-cogent/python3-cogent3_2023.2.12a1+dfsg-2+deb12u1_arm64.deb

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

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2023.2.12a1+dfsg-2+deb12u1 / amd64Observed Sep 1, 2026 to Sep 1, 2026

Verification status: Metadata observed; artifact bytes were not independently fetched or hashed by this catalog import. The digest below is source-reported.

Source-reported sha256: 046584868fc9d4109b8d8ec25a8f1ab81f1a6276b6559ba76a224850660a7a5b

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printf '%s  %s\n' '046584868fc9d4109b8d8ec25a8f1ab81f1a6276b6559ba76a224850660a7a5b' 'python3-cogent3_2023.2.12a1+dfsg-2+deb12u1_amd64.deb' | sha256sum --check --strict -

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Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

2023.2.12a1+dfsg-2+deb12u1 / arm64Observed Sep 1, 2026 to Sep 1, 2026

Verification status: Metadata observed; artifact bytes were not independently fetched or hashed by this catalog import. The digest below is source-reported.

Source-reported sha256: 9ae86b4e30b166201e4ec816849c647433a3d6d1c6b410594c720cca84085c65

After downloading that exact artifact, compare its bytes with the source-reported expected digest:

printf '%s  %s\n' '9ae86b4e30b166201e4ec816849c647433a3d6d1c6b410594c720cca84085c65' 'python3-cogent3_2023.2.12a1+dfsg-2+deb12u1_arm64.deb' | sha256sum --check --strict -

A match establishes equality with the repository metadata value. It does not establish safety or catalog-side artifact retrieval.

Field source: Debian 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00

Catalog record completeness

The completeness score measures metadata coverage, not software quality, security, compatibility, or suitability.

Summary and description: 25/25
Artifact path and source digest: 25/25
Dependency metadata: 15/15
Package-file index: 15/15
Homepage: 5/5
License text: 0/5
Source package or maintainer: 10/10

Recorded total: 95/100

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5, Debian 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00. The cross-OS mapping is catalog-derived from the source-reported homepage; it does not establish authorship or publisher identity

Sources and provenance

Field-source links above resolve here. Each source entry names the metadata publisher, trust tier, exact snapshot revision, signature result, and observation time; catalog-derived mappings are labeled separately.

Debian 12 (Bookworm) main amd64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-amd64/Packages.xz
Expected SHA-256: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Observed SHA-256: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Result: match verified
Debian 12 (Bookworm) main arm64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-arm64/Packages.xz
Expected SHA-256: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Observed SHA-256: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Result: match verified