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]

Шляхи файлів пакета (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

Використати цей пакет

OpenFactory може завантажити цю операційну систему у віртуальній машині браузера або почати збірку образу з рідною назвою пакета з цього запису.

Спробувати Debian 13 (Trixie) у браузері Зібрати образ, що містить augustus

Версії, набори та репозиторії

Кожен рядок: метадані індексу пакетів для однієї версії, архітектури, набору й репозиторію. Назви, URL і розміри зі джерела; посилання є змінним місцем отримання, не перерозповсюдженням 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

Контрольні суми й дати спостереження

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

Повнота запису каталогу

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

Джерела та походження

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