Debian 13 (Trixie) native package

augustus

gene prediction in eukaryotic genomes

Packages / Debian 13 (Trixie) / science / augustus

Package: augustus (3.5.0+dfsg-5)

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [bioinf.uni-greifswald.de]

gene prediction in eukaryotic genomes

Other Packages Related to augustus:

dep: [libbamtools2.5.2] (>= 2.5.2+dfsg)
dynamic library for manipulating BAM (genome alignment) files
dep: [libboost-iostreams1.83.0] (>= 1.83.0)
Boost.Iostreams Library
dep: [libc6] (>= 2.38)
GNU C Library: Shared libraries
dep: [libcolamd3] (>= 1:7.0.1)
column approximate minimum degree ordering library for sparse matrices
dep: [libgcc-s1] (>= 3.0)
GCC support library
dep: [libgsl28] (>= 2.8+dfsg)
GNU Scientific Library (GSL) -- library package
dep: [libhts3t64] (>= 1.17)
C library for high-throughput sequencing data formats
dep: [libmariadb3] (>= 3.0.0)
MariaDB database client library
dep: [libmysql++3t64]
MySQL C++ library bindings (runtime)
dep: [libsqlite3-0] (>= 3.5.9)
SQLite 3 shared library
dep: [libstdc++6] (>= 14)
GNU Standard C++ Library v3
dep: [augustus-data]
data files for AUGUSTUS

rec: [samtools]
processing sequence alignments in SAM, BAM and CRAM formats

sug: [cdbfasta]
Constant DataBase indexing and retrieval tools for multi-FASTA files
sug: [diamond-aligner]
accelerated BLAST compatible local sequence aligner
sug: [libfile-which-perl]
Perl module for searching paths for executable programs
sug: [libparallel-forkmanager-perl]
simple parallel processing fork manager for Perl
sug: [libyaml-perl]
YAML Ain't Markup Language
sug: [libdbd-mysql-perl]
Perl5 database interface to the MariaDB/MySQL database
sug: [python3-biopython]
Python3 library for bioinformatics

Download augustus

Architecture	Package Size	Installed Size	Files
amd64	2.1 MiB	11 MiB	[list of files]
arm64	1.8 MiB	11 MiB	[list of files]

Chemins de fichiers du paquet (142)

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/aln2wig
/usr/bin/augustus
/usr/bin/bam2hints
/usr/bin/bam2wig
/usr/bin/compileSpliceCands
/usr/bin/etraining
/usr/bin/fastBlockSearch
/usr/bin/filterBam
/usr/bin/getSeq
/usr/bin/homGeneMapping
/usr/bin/joingenes
/usr/bin/load2db
/usr/bin/load2sqlitedb
/usr/bin/pp_simScore
/usr/bin/prepareAlign
/usr/share/augustus/scripts/aa2nonred.pl
/usr/share/augustus/scripts/add_name_to_gff3.pl
/usr/share/augustus/scripts/augustify.py
/usr/share/augustus/scripts/augustus2browser.pl
/usr/share/augustus/scripts/augustus2gbrowse.pl
/usr/share/augustus/scripts/autoAug.pl
/usr/share/augustus/scripts/autoAugPred.pl
/usr/share/augustus/scripts/autoAugTrain.pl
/usr/share/augustus/scripts/bamToWig.py
/usr/share/augustus/scripts/bedgraph2wig.pl
/usr/share/augustus/scripts/blat2gbrowse.pl
/usr/share/augustus/scripts/blat2hints.pl
/usr/share/augustus/scripts/block2prfl.pl
/usr/share/augustus/scripts/cegma2gff.pl
/usr/share/augustus/scripts/checkParamArchive.pl
/usr/share/augustus/scripts/checkUTR
/usr/share/augustus/scripts/cleanDOSfasta.pl
/usr/share/augustus/scripts/clusterAndSplitGenes.pl
/usr/share/augustus/scripts/compare_masking.pl
/usr/share/augustus/scripts/computeFlankingRegion.pl
/usr/share/augustus/scripts/createAugustusJoblist.pl
/usr/share/augustus/scripts/del_from_prfl.pl
/usr/share/augustus/scripts/evalCGP.pl
/usr/share/augustus/scripts/eval_dualdecomp.pl
/usr/share/augustus/scripts/eval_multi_gtf.pl
/usr/share/augustus/scripts/exonerate2hints.pl
/usr/share/augustus/scripts/exoniphyDb2hints.pl
/usr/share/augustus/scripts/extractAnno.py
/usr/share/augustus/scripts/extractTranscriptEnds.pl
/usr/share/augustus/scripts/filterGenesIn_mRNAname.pl
/usr/share/augustus/scripts/filterGenesIn.pl
/usr/share/augustus/scripts/filterGenesOut_mRNAname.pl
/usr/share/augustus/scripts/filterGenes.pl
/usr/share/augustus/scripts/filterInFrameStopCodons.pl
/usr/share/augustus/scripts/filterMaf.pl
/usr/share/augustus/scripts/filter-ppx.pl
/usr/share/augustus/scripts/filterPSL.pl
/usr/share/augustus/scripts/filterShrimp.pl
/usr/share/augustus/scripts/filterSpliceHints.pl
/usr/share/augustus/scripts/findGffNamesInFasta.pl
/usr/share/augustus/scripts/findRepetitiveProtSeqs.py
/usr/share/augustus/scripts/fix_in_frame_stop_codon_genes.py
/usr/share/augustus/scripts/fix_joingenes_gtf.pl
/usr/share/augustus/scripts/gbrowse.conf
/usr/share/augustus/scripts/gbrowseold2gff3.pl
/usr/share/augustus/scripts/gbSmallDNA2gff.pl
/usr/share/augustus/scripts/getAnnoFastaFromJoingenes.py
/usr/share/augustus/scripts/getAnnoFasta.pl
/usr/share/augustus/scripts/getLinesMatching.pl
/usr/share/augustus/scripts/get_loci_from_gb.pl
/usr/share/augustus/scripts/gff2gbSmallDNA.pl
/usr/share/augustus/scripts/gff2ps_mycustom
/usr/share/augustus/scripts/gffGetmRNA.pl
/usr/share/augustus/scripts/gp2othergp.pl
/usr/share/augustus/scripts/gtf2aa.pl
/usr/share/augustus/scripts/gtf2bed.pl
/usr/share/augustus/scripts/gtf2gff.pl
/usr/share/augustus/scripts/gth2gtf.pl
/usr/share/augustus/scripts/hal2maf_split.pl
/usr/share/augustus/scripts/helpMod.pm
/usr/share/augustus/scripts/join_aug_pred.pl
/usr/share/augustus/scripts/join_mult_hints.pl
/usr/share/augustus/scripts/joinPeptides.pl
/usr/share/augustus/scripts/maf2conswig.pl
/usr/share/augustus/scripts/makeMatchLists.pl
/usr/share/augustus/scripts/makeUtrTrainingSet.pl
/usr/share/augustus/scripts/maskNregions.pl
/usr/share/augustus/scripts/merge_masking.pl
/usr/share/augustus/scripts/moveParameters.pl
/usr/share/augustus/scripts/msa2prfl.pl
/usr/share/augustus/scripts/new_species.pl
/usr/share/augustus/scripts/optimize_augustus.pl
/usr/share/augustus/scripts/opt_init_and_term_probs.pl
/usr/share/augustus/scripts/parseSim4Output.pl
/usr/share/augustus/scripts/partition_gtf2gb.pl
/usr/share/augustus/scripts/pasapolyA2hints.pl
/usr/share/augustus/scripts/peptides2alternatives.pl
/usr/share/augustus/scripts/peptides2hints.pl
/usr/share/augustus/scripts/phastconsDB2hints.pl
/usr/share/augustus/scripts/polyA2hints.pl
/usr/share/augustus/scripts/prints2prfl.pl
/usr/share/augustus/scripts/pslMap.pl
/usr/share/augustus/scripts/randomSplit.pl
/usr/share/augustus/scripts/README.autoAug
/usr/share/augustus/scripts/rename_species.pl
/usr/share/augustus/scripts/retroDB2hints.pl
/usr/share/augustus/scripts/rmRedundantHints.pl
/usr/share/augustus/scripts/runAllSim4.pl
/usr/share/augustus/scripts/samMap.pl
/usr/share/augustus/scripts/scipiogff2gff.pl
/usr/share/augustus/scripts/setStopCodonFreqs.pl
/usr/share/augustus/scripts/simpleFastaHeaders.pl
/usr/share/augustus/scripts/simplifyFastaHeaders.pl
/usr/share/augustus/scripts/SplicedAlignment.pm
/usr/share/augustus/scripts/splitMfasta.pl
/usr/share/augustus/scripts/split_wiggle.pl
/usr/share/augustus/scripts/stringtie2fa.py
/usr/share/augustus/scripts/summarizeACGTcontent.pl
/usr/share/augustus/scripts/transMap2hints.pl
/usr/share/augustus/scripts/uniquePeptides.pl
/usr/share/augustus/scripts/utrgff2gbrowse.pl
/usr/share/augustus/scripts/webserver-results.head
/usr/share/augustus/scripts/webserver-results.tail
/usr/share/augustus/scripts/weedMaf.pl
/usr/share/augustus/scripts/wig2hints.pl
/usr/share/augustus/scripts/wigchoose.pl
/usr/share/augustus/scripts/writeResultsPage.pl
/usr/share/augustus/scripts/yaml2gff.1.4.pl
/usr/share/doc/augustus/changelog.Debian.gz
/usr/share/doc/augustus/changelog.gz
/usr/share/doc/augustus/copyright
/usr/share/doc/augustus/HISTORY.TXT.gz
/usr/share/man/man1/aln2wig.1.gz
/usr/share/man/man1/augustus.1.gz
/usr/share/man/man1/bam2hints.1.gz
/usr/share/man/man1/bam2wig.1.gz
/usr/share/man/man1/compileSpliceCands.1.gz
/usr/share/man/man1/etraining.1.gz
/usr/share/man/man1/fastBlockSearch.1.gz
/usr/share/man/man1/filterBam.1.gz
/usr/share/man/man1/getSeq.1.gz
/usr/share/man/man1/homGeneMapping.1.gz
/usr/share/man/man1/joingenes.1.gz
/usr/share/man/man1/load2db.1.gz
/usr/share/man/man1/load2sqlitedb.1.gz
/usr/share/man/man1/pp_simScore.1.gz
/usr/share/man/man1/prepareAlign.1.gz

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 augustus

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
3.5.0+dfsg-5	trixie / main	amd64	Debian 13 · main · amd64	2.1 MiB	11 MiB	pool/main/a/augustus/augustus_3.5.0+dfsg-5_amd64.deb
3.5.0+dfsg-5	trixie / main	arm64	Debian 13 · main · arm64	1.8 MiB	11 MiB	pool/main/a/augustus/augustus_3.5.0+dfsg-5_arm64.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.

3.5.0+dfsg-5 / 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: aafc03430d2e4257d0854e56f239d3a522d37790af08108c8b8828d6ba330705

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

printf '%s  %s\n' 'aafc03430d2e4257d0854e56f239d3a522d37790af08108c8b8828d6ba330705' 'augustus_3.5.0+dfsg-5_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

3.5.0+dfsg-5 / 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: f0150196ad3b991039f195281515f26220da7ef1b6fce75bb58342543d672974

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

printf '%s  %s\n' 'f0150196ad3b991039f195281515f26220da7ef1b6fce75bb58342543d672974' 'augustus_3.5.0+dfsg-5_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

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, 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

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
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