Debian 13 (Trixie) native package

parsnp

rapid core genome multi-alignment

Packages / Debian 13 (Trixie) / science / parsnp

Package: parsnp (2.1.3+dfsg-1)

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [harvest.readthedocs.org]

rapid core genome multi-alignment

Other Packages Related to parsnp:

dep: [libc6] (>= 2.38)
GNU C Library: Shared libraries
dep: [libgcc-s1] (>= 3.0)
GCC support library
dep: [libgomp1] (>= 6)
GCC OpenMP (GOMP) support library
dep: [libmuscle1] (>= 3.7+4565)
multiple alignment library for protein sequences
dep: [libstdc++6] (>= 14)
GNU Standard C++ Library v3
dep: [python3] [any]
interactive high-level object-oriented language (default python3 version)
dep: [python3-biopython]
Python3 library for bioinformatics
dep: [python3-numpy]
Python library for numerical computations (Python 3)
dep: [python3-pyspoa]
Python bindings to spoa
dep: [python3-tqdm]
fast, extensible progress bar for Python 3 and CLI tool
dep: [fasttree]
phylogenetic trees from alignments of nucleotide or protein sequences
dep: [harvest-tools]
archiving and postprocessing for reference-compressed genomic multi-alignments
dep: [mummer]
Efficient sequence alignment of full genomes
dep: [phipack]
PHI test and other tests of recombination
dep: [python3]
interactive high-level object-oriented language (default python3 version)
dep: [raxml]
Randomized Axelerated Maximum Likelihood of phylogenetic trees
dep: [time]
GNU time program for measuring CPU resource usage

rec: [python3-dendropy]
DendroPy Phylogenetic Computing Library (Python 3)

Download parsnp

Architecture	Package Size	Installed Size	Files
amd64	209 KiB	1.9 MiB	[list of files]
arm64	196 KiB	1.9 MiB	[list of files]

Percorsi file del pacchetto (61)

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/parsnp
/usr/lib/parsnp/parsnp_core
/usr/lib/python3/dist-packages/parsnp/extend.py
/usr/lib/python3/dist-packages/parsnp/logger.py
/usr/lib/python3/dist-packages/parsnp/partition.py
/usr/share/doc/parsnp/changelog.Debian.gz
/usr/share/doc/parsnp/copyright
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_1_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_12_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_15_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_16_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_17_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_18_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_19_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_21_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_2_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_25_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_3_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_4_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Bisha_1_2012.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Buraidah_1_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/EMC_2012.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/England1.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/England-Qatar_2012.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/FRA-UAE.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Hafr-Al-Batin_1_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Hafr-Al-Batin_2_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Hafr-Al_Batin_6_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Indiana-USA-1_Saudi_Arabia_2014.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Jeddah_1_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Jordan-N3_2012.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/KF192507.1.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/KFU-HKU_13.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/KFU-HKU_19Dam.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/KFU-HKU_1.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/KJ477102.1.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/KSA-CAMEL-363.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/KSA-CAMEL-376.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/KSA-CAMEL-378.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/KSA-CAMEL-503.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/KSA-CAMEL-505.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/NC_019843.2.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Qatar3.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Qatar4.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_1_2012.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_14_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_2_2012.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_3_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_4_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_5_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_9_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Taif_1_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/genomes/Wadi-Ad-Dawasir_1_2013.fna
/usr/share/doc/parsnp/examples/mers_virus/ref/England1.fna
/usr/share/doc/parsnp/examples/mers_virus/ref/England1.gbk
/usr/share/doc/parsnp/NEWS.gz
/usr/share/doc/parsnp/README.md.gz
/usr/share/doc/parsnp/README.test
/usr/share/doc/parsnp/run-unit-test
/usr/share/man/man1/parsnp.1.gz
/usr/share/parsnp/template.ini

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

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Versioni, suite e repository

Ogni riga è metadato dell'indice pacchetti per una versione, architettura, suite e repository. Nomi, URL e dimensioni arrivano dalla fonte; un link è un punto di recupero mutabile, non una redistribuzione OpenFactory.

Version	Release	Architecture	Repository	Package size	Installed size	Publisher repository artifact
2.1.3+dfsg-1	trixie / main	amd64	Debian 13 · main · amd64	209 KiB	1.9 MiB	pool/main/p/parsnp/parsnp_2.1.3+dfsg-1_amd64.deb
2.1.3+dfsg-1	trixie / main	arm64	Debian 13 · main · arm64	196 KiB	1.9 MiB	pool/main/p/parsnp/parsnp_2.1.3+dfsg-1_arm64.deb

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

Checksum e date di osservazione

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.

2.1.3+dfsg-1 / 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: 70d32d1ca5628174aa799c41632ae8df46b5a2135864bb86017f0c502617b368

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

printf '%s  %s\n' '70d32d1ca5628174aa799c41632ae8df46b5a2135864bb86017f0c502617b368' 'parsnp_2.1.3+dfsg-1_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

2.1.3+dfsg-1 / 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: 6d0fb87eadc47b2a02ee062b36cf647d29d97cbf3fadbbcff3c4d90089ed20b9

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

printf '%s  %s\n' '6d0fb87eadc47b2a02ee062b36cf647d29d97cbf3fadbbcff3c4d90089ed20b9' 'parsnp_2.1.3+dfsg-1_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 13 (Trixie) main arm64 revision trixie-main-arm64:753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908

Completezza del record

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, Debian 13 (Trixie) main arm64 revision trixie-main-arm64:753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908. The cross-OS mapping is catalog-derived from the source-reported homepage; it does not establish authorship or publisher identity

Fonti e provenienza

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
Debian 13 (Trixie) main arm64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision trixie-main-arm64:753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908
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-arm64/Packages.xz
Expected SHA-256: 753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908
Observed SHA-256: 753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908
Result: match verified