Debian 13 (Trixie) native package

gubbins

phylogenetic analysis of genome sequences

Packages / Debian 13 (Trixie) / science / gubbins

Package: gubbins (3.4-2)

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [sanger-pathogens.github.io]

phylogenetic analysis of genome sequences

Other Packages Related to gubbins:

dep: [libc6] (>= 2.34)
GNU C Library: Shared libraries
dep: [zlib1g] (>= 1:1.1.4)
compression library - runtime
dep: [python3-biopython]
Python3 library for bioinformatics
dep: [python3-dendropy]
DendroPy Phylogenetic Computing Library (Python 3)
dep: [python3-multiprocess]
better multiprocessing and multithreading in Python
dep: [python3-numpy]
Python library for numerical computations (Python 3)
dep: [python3-scipy]
scientific tools for Python 3
dep: [python3] [any]
interactive high-level object-oriented language (default python3 version)
dep: [python3]
interactive high-level object-oriented language (default python3 version)
dep: [python3-pkg-resources]
Package Discovery and Resource Access using pkg_resources
dep: [raxml]
Randomized Axelerated Maximum Likelihood of phylogenetic trees

rec: [iqtree]
efficient phylogenetic software by maximum likelihood
rec: [fasttree]
phylogenetic trees from alignments of nucleotide or protein sequences

sug: [r-base-core]
GNU R core of statistical computation and graphics system

Download gubbins

Architecture	Package Size	Installed Size	Files
amd64	93 KiB	483 KiB	[list of files]

Chemins de fichiers du paquet (44)

Paths come from the repository package-file index for the observed builds. They describe archive/package associations, not every file that will exist on a running system after maintainer scripts, alternatives, generated state, diversions, or installation choices.

/usr/bin/run_gubbins
/usr/lib/gubbins/gubbins
/usr/lib/x86_64-linux-gnu/libgubbins.so
/usr/lib/x86_64-linux-gnu/libgubbins.so.0
/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1
/usr/share/doc/gubbins/changelog.Debian.gz
/usr/share/doc/gubbins/changelog.gz
/usr/share/doc/gubbins/copyright
/usr/share/gubbins/count_recombinations_per_gene.py
/usr/share/gubbins/extract_gubbins_clade.py
/usr/share/gubbins/extract_recombinant_sequences.py
/usr/share/gubbins/generate_files_for_clade_analysis.py
/usr/share/gubbins/generate_ska_alignment.py
/usr/share/gubbins/gubbins-3.4.egg-info/dependency_links.txt
/usr/share/gubbins/gubbins-3.4.egg-info/entry_points.txt
/usr/share/gubbins/gubbins-3.4.egg-info/PKG-INFO
/usr/share/gubbins/gubbins-3.4.egg-info/requires.txt
/usr/share/gubbins/gubbins-3.4.egg-info/top_level.txt
/usr/share/gubbins/gubbins_alignment_checker.py
/usr/share/gubbins/gubbins/common.py
/usr/share/gubbins/gubbins/__init__.py
/usr/share/gubbins/gubbins/PreProcessFasta.py
/usr/share/gubbins/gubbins/pyjar.py
/usr/share/gubbins/gubbins/run_gubbins.py
/usr/share/gubbins/gubbins/tests/__init__.py
/usr/share/gubbins/gubbins/tests/test_alignment_python_methods.py
/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py
/usr/share/gubbins/gubbins/tests/test_dependencies.py
/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py
/usr/share/gubbins/gubbins/tests/test_python_scripts.py
/usr/share/gubbins/gubbins/tests/test_treebuilders.py
/usr/share/gubbins/gubbins/tests/test_tree_methods.py
/usr/share/gubbins/gubbins/tests/test_utils.py
/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py
/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py
/usr/share/gubbins/gubbins/treebuilders.py
/usr/share/gubbins/gubbins/utils.py
/usr/share/gubbins/gubbins/ValidateFastaAlignment.py
/usr/share/gubbins/mask_gubbins_aln.py
/usr/share/gubbins/plot_gubbins.R
/usr/share/gubbins/run_gubbins.py
/usr/share/lintian/overrides/gubbins
/usr/share/man/man1/run_gubbins.1.gz
/usr/share/python3/runtime.d/gubbins.rtupdate

Field source: Debian 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3

Utiliser ce paquet

OpenFactory peut démarrer ce système d'exploitation dans une machine virtuelle du navigateur, ou lancer une construction qui inclut le nom natif du paquet de cet enregistrement.

Essayer Debian 13 (Trixie) dans le navigateur Construire une image qui inclut gubbins

Versions, suites et dépôts

Chaque ligne est une métadonnée d'index pour une version, une architecture, une suite et un dépôt. Noms, URL et tailles viennent de la source ; un lien est un emplacement de récupération mutable, pas une redistribution OpenFactory.

Version	Release	Architecture	Repository	Package size	Installed size	Publisher repository artifact
3.4-2	trixie / main	amd64	Debian 13 · main · amd64	93 KiB	483 KiB	pool/main/g/gubbins/gubbins_3.4-2_amd64.deb

Field source: Debian 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3

Empreintes et dates d'observation

For an APT source, signature verification authenticates the repository metadata chain and the Packages index containing this source-reported artifact digest. It does not certify package safety.

3.4-2 / 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: 5ee9fe0f7827ae29857251707e866f5a48fab4db3e1d21a26bbc8624053c18da

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

printf '%s  %s\n' '5ee9fe0f7827ae29857251707e866f5a48fab4db3e1d21a26bbc8624053c18da' 'gubbins_3.4-2_amd64.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 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3

Complétude de la fiche

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 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3. The cross-OS mapping is catalog-derived from the source-reported homepage; it does not establish authorship or publisher identity

Sources et 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 13 (Trixie) main amd64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3
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/trixie/InRelease
Signed-object SHA-256
98b25b5cd185c59d34aa6e4c3e9b5b8f01bbe9d104fe2dcfbcd30dc0a14a59ed
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: 3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3
Observed SHA-256: 3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3
Result: match verified