Debian 13 (Trixie) native package

paleomix

pipelines and tools for the processing of ancient and modern HTS data

Packages / Debian 13 (Trixie) / science / paleomix

Package: paleomix (1.3.8-2)

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [geogenetics.ku.dk]

pipelines and tools for the processing of ancient and modern HTS data

Other Packages Related to paleomix:

dep: [python3-coloredlogs]
colored terminal output for Python 3's logging module
dep: [python3-configargparse]
replacement for argparse with config files and environment variables
dep: [python3-pysam]
interface for the SAM/BAM sequence alignment and mapping format (Python 3)
dep: [python3-ruamel.yaml]
Roundtrip YAML parser/emitter (Python 3 module)
dep: [python3-setproctitle]
Setproctitle implementation for Python 3
dep: [python3] [any]
interactive high-level object-oriented language (default python3 version)
dep: [adapterremoval]
rapid adapter trimming, identification, and read merging of gene sequences
dep: [bedtools]
suite of utilities for comparing genomic features
dep: [bowtie2]
ultrafast memory-efficient short read aligner
dep: [bwa]
Burrows-Wheeler Aligner
dep: [bcftools]
genomic variant calling and manipulation of VCF/BCF files
dep: [examl]
Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
dep: [mafft]
Multiple alignment program for amino acid or nucleotide sequences
dep: [mapdamage]
tracking and quantifying damage patterns in ancient DNA sequences
dep: [phylip]
package of programs for inferring phylogenies
dep: [picard-tools]
Command line tools to manipulate SAM and BAM files
dep: [r-base-core]
GNU R core of statistical computation and graphics system
dep: [radiant]
explore hierarchical metagenomic data with zoomable pie charts
dep: [raxml]
Randomized Axelerated Maximum Likelihood of phylogenetic trees
dep: [samtools]
processing sequence alignments in SAM, BAM and CRAM formats

Download paleomix

Architecture	Package Size	Installed Size	Files
amd64	961 KiB	2.0 MiB	[list of files]
arm64	961 KiB	2.0 MiB	[list of files]

Percorsi file del pacchetto (206)

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/paleomix
/usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/dependency_links.txt
/usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/entry_points.txt
/usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/not-zip-safe
/usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/PKG-INFO
/usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/requires.txt
/usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/top_level.txt
/usr/lib/python3/dist-packages/paleomix/atomiccmd/builder.py
/usr/lib/python3/dist-packages/paleomix/atomiccmd/command.py
/usr/lib/python3/dist-packages/paleomix/atomiccmd/__init__.py
/usr/lib/python3/dist-packages/paleomix/atomiccmd/pprint.py
/usr/lib/python3/dist-packages/paleomix/atomiccmd/sets.py
/usr/lib/python3/dist-packages/paleomix/common/argparse.py
/usr/lib/python3/dist-packages/paleomix/common/bamfiles.py
/usr/lib/python3/dist-packages/paleomix/common/bedtools.py
/usr/lib/python3/dist-packages/paleomix/common/fileutils.py
/usr/lib/python3/dist-packages/paleomix/common/formats/_common.py
/usr/lib/python3/dist-packages/paleomix/common/formats/fasta.py
/usr/lib/python3/dist-packages/paleomix/common/formats/fastq.py
/usr/lib/python3/dist-packages/paleomix/common/formats/_graph.py
/usr/lib/python3/dist-packages/paleomix/common/formats/__init__.py
/usr/lib/python3/dist-packages/paleomix/common/formats/msa.py
/usr/lib/python3/dist-packages/paleomix/common/formats/newick.py
/usr/lib/python3/dist-packages/paleomix/common/formats/phylip.py
/usr/lib/python3/dist-packages/paleomix/common/__init__.py
/usr/lib/python3/dist-packages/paleomix/common/logging.py
/usr/lib/python3/dist-packages/paleomix/common/makefile.py
/usr/lib/python3/dist-packages/paleomix/common/procs.py
/usr/lib/python3/dist-packages/paleomix/common/rtools.py
/usr/lib/python3/dist-packages/paleomix/common/sampling.py
/usr/lib/python3/dist-packages/paleomix/common/sequences.py
/usr/lib/python3/dist-packages/paleomix/common/system.py
/usr/lib/python3/dist-packages/paleomix/common/testing.py
/usr/lib/python3/dist-packages/paleomix/common/text.py
/usr/lib/python3/dist-packages/paleomix/common/timer.py
/usr/lib/python3/dist-packages/paleomix/common/utilities.py
/usr/lib/python3/dist-packages/paleomix/common/vcffilter.py
/usr/lib/python3/dist-packages/paleomix/common/vcfwrap.py
/usr/lib/python3/dist-packages/paleomix/common/versions.py
/usr/lib/python3/dist-packages/paleomix/__init__.py
/usr/lib/python3/dist-packages/paleomix/main.py
/usr/lib/python3/dist-packages/paleomix/nodegraph.py
/usr/lib/python3/dist-packages/paleomix/node.py
/usr/lib/python3/dist-packages/paleomix/nodes/adapterremoval.py
/usr/lib/python3/dist-packages/paleomix/nodes/bedtools.py
/usr/lib/python3/dist-packages/paleomix/nodes/bowtie2.py
/usr/lib/python3/dist-packages/paleomix/nodes/bwa.py
/usr/lib/python3/dist-packages/paleomix/nodes/commands.py
/usr/lib/python3/dist-packages/paleomix/nodes/examl.py
/usr/lib/python3/dist-packages/paleomix/nodes/formats.py
/usr/lib/python3/dist-packages/paleomix/nodes/__init__.py
/usr/lib/python3/dist-packages/paleomix/nodes/mafft.py
/usr/lib/python3/dist-packages/paleomix/nodes/mapdamage.py
/usr/lib/python3/dist-packages/paleomix/nodes/newick.py
/usr/lib/python3/dist-packages/paleomix/nodes/phylip.py
/usr/lib/python3/dist-packages/paleomix/nodes/picard.py
/usr/lib/python3/dist-packages/paleomix/nodes/raxml.py
/usr/lib/python3/dist-packages/paleomix/nodes/samtools.py
/usr/lib/python3/dist-packages/paleomix/nodes/sequences.py
/usr/lib/python3/dist-packages/paleomix/nodes/validation.py
/usr/lib/python3/dist-packages/paleomix/pipeline.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/config.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/__init__.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/makefile.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/mkfile.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/nodes.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/__init__.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/lane.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/library.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/prefix.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/reads.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/sample.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/statistics.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/summary.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/target.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/paths.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/pipeline.py
/usr/lib/python3/dist-packages/paleomix/pipelines/bam/trim_pipeline.py
/usr/lib/python3/dist-packages/paleomix/pipelines/__init__.py
/usr/lib/python3/dist-packages/paleomix/pipelines/phylo/config.py
/usr/lib/python3/dist-packages/paleomix/pipelines/phylo/example.py
/usr/lib/python3/dist-packages/paleomix/pipelines/phylo/__init__.py
/usr/lib/python3/dist-packages/paleomix/pipelines/phylo/makefile.py
/usr/lib/python3/dist-packages/paleomix/pipelines/phylo/mkfile.py
/usr/lib/python3/dist-packages/paleomix/pipelines/phylo/parts/genotype.py
/usr/lib/python3/dist-packages/paleomix/pipelines/phylo/parts/__init__.py
/usr/lib/python3/dist-packages/paleomix/pipelines/phylo/parts/msa.py
/usr/lib/python3/dist-packages/paleomix/pipelines/phylo/parts/phylo.py
/usr/lib/python3/dist-packages/paleomix/pipelines/phylo/pipeline.py
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/build_db.py
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/build_mito.py
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/build_tped.py
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/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/config.py
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/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/common.py
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/__init__.py
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/mitochondria.py
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/nuclear.py
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/report.py
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/summary.py
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/pipeline.py
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_01.fastq.gz
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/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_01.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_02.fastq.gz
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/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.truncated.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.singleton.truncated.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_01.fastq.gz
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/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_01.fastq.gz
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/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/prefixes/rCRS.fasta
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/makefile.yaml
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/bonobo.fasta
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/chimpanzee.fasta
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/gorilla.fasta
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta.fai
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/sumatran_orangutan.fasta
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/white_handed_gibbon.fasta
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/setup.sh
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/setup.sh
/usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py
/usr/lib/python3/dist-packages/paleomix/resources/__init__.py
/usr/lib/python3/dist-packages/paleomix/resources/reports/zonkey/report.css
/usr/lib/python3/dist-packages/paleomix/resources/rscripts/common/requires.r
/usr/lib/python3/dist-packages/paleomix/resources/rscripts/zonkey/admixture.r
/usr/lib/python3/dist-packages/paleomix/resources/rscripts/zonkey/coverage.r
/usr/lib/python3/dist-packages/paleomix/resources/rscripts/zonkey/pca.r
/usr/lib/python3/dist-packages/paleomix/resources/rscripts/zonkey/tinytree.r
/usr/lib/python3/dist-packages/paleomix/resources/rscripts/zonkey/treemix.r
/usr/lib/python3/dist-packages/paleomix/tools/bam_stats/common.py
/usr/lib/python3/dist-packages/paleomix/tools/bam_stats/coverage.py
/usr/lib/python3/dist-packages/paleomix/tools/bam_stats/__init__.py
/usr/lib/python3/dist-packages/paleomix/tools/cleanup.py
/usr/lib/python3/dist-packages/paleomix/tools/coverage.py
/usr/lib/python3/dist-packages/paleomix/tools/depths.py
/usr/lib/python3/dist-packages/paleomix/tools/dupcheck.py
/usr/lib/python3/dist-packages/paleomix/tools/factory.py
/usr/lib/python3/dist-packages/paleomix/tools/gtf_to_bed.py
/usr/lib/python3/dist-packages/paleomix/tools/__init__.py
/usr/lib/python3/dist-packages/paleomix/tools/rmdup_collapsed.py
/usr/lib/python3/dist-packages/paleomix/tools/validate_fastq.py
/usr/lib/python3/dist-packages/paleomix/tools/vcf_filter.py
/usr/lib/python3/dist-packages/paleomix/tools/vcf_to_fasta.py
/usr/lib/python3/dist-packages/paleomix/yaml.py
/usr/share/doc/paleomix/changelog.Debian.gz
/usr/share/doc/paleomix/changelog.gz
/usr/share/doc/paleomix/copyright
/usr/share/doc/paleomix/README.rst
/usr/share/doc/paleomix/README.test
/usr/share/doc/paleomix/run-unit-test
/usr/share/doc/paleomix/tests/atomiccmd_test/builder_test.py.gz
/usr/share/doc/paleomix/tests/atomiccmd_test/command_test.py.gz
/usr/share/doc/paleomix/tests/atomiccmd_test/__init__.py
/usr/share/doc/paleomix/tests/atomiccmd_test/pprint_test.py.gz
/usr/share/doc/paleomix/tests/atomiccmd_test/sets_test.py.gz
/usr/share/doc/paleomix/tests/common_tests/bedtools_test.py.gz
/usr/share/doc/paleomix/tests/common_tests/formats_tests/fasta_test.py.gz
/usr/share/doc/paleomix/tests/common_tests/formats_tests/fastq_test.py.gz
/usr/share/doc/paleomix/tests/common_tests/formats_tests/__init__.py
/usr/share/doc/paleomix/tests/common_tests/formats_tests/msa_test.py.gz
/usr/share/doc/paleomix/tests/common_tests/formats_tests/newick_test.py.gz
/usr/share/doc/paleomix/tests/common_tests/formats_tests/phylip_test.py.gz
/usr/share/doc/paleomix/tests/common_tests/__init__.py
/usr/share/doc/paleomix/tests/common_tests/makefile_test.py.gz
/usr/share/doc/paleomix/tests/common_tests/sampling_test.py.gz
/usr/share/doc/paleomix/tests/common_tests/sequences_test.py.gz
/usr/share/doc/paleomix/tests/common_tests/text_test.py.gz
/usr/share/doc/paleomix/tests/common_tests/utilities_test.py.gz
/usr/share/doc/paleomix/tests/common_tests/versions_test.py.gz
/usr/share/doc/paleomix/tests/data/empty_file_1
/usr/share/doc/paleomix/tests/data/empty_file_2
/usr/share/doc/paleomix/tests/data/rCRS.fasta.fai
/usr/share/doc/paleomix/tests/data/rCRS.fasta.gz
/usr/share/doc/paleomix/tests/nodegraph_test.py.gz
/usr/share/doc/paleomix/tests/node_test.py.gz
/usr/share/doc/paleomix/tests/README.rst
/usr/share/doc/paleomix/tests/tools_test/factory_test.py
/usr/share/lintian/overrides/paleomix
/usr/share/man/man1/bam_pipeline.1.gz
/usr/share/man/man1/bam_rmdup_collapsed.1.gz
/usr/share/man/man1/conv_gtf_to_bed.1.gz
/usr/share/man/man1/paleomix.1.gz
/usr/share/man/man1/phylo_pipeline.1.gz
/usr/share/man/man1/trim_pipeline.1.gz

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

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Versioni, suite e repository

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Version	Release	Architecture	Repository	Package size	Installed size	Publisher repository artifact
1.3.8-2	trixie / main	amd64	Debian 13 · main · amd64	961 KiB	2.0 MiB	pool/main/p/paleomix/paleomix_1.3.8-2_amd64.deb
1.3.8-2	trixie / main	arm64	Debian 13 · main · arm64	961 KiB	2.0 MiB	pool/main/p/paleomix/paleomix_1.3.8-2_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.

1.3.8-2 / 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: 56fcce16061450d75d95b3db3d8169aee8f8e810f5ac2a725ea57c7dce44864e

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

printf '%s  %s\n' '56fcce16061450d75d95b3db3d8169aee8f8e810f5ac2a725ea57c7dce44864e' 'paleomix_1.3.8-2_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

1.3.8-2 / 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: 0ed87162c2436a6c4498351ba316b5af68f8248891ca77478595a8aa4e86799a

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

printf '%s  %s\n' '0ed87162c2436a6c4498351ba316b5af68f8248891ca77478595a8aa4e86799a' 'paleomix_1.3.8-2_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