Debian 12 (Bookworm) native package

paleomix

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

Packages / Debian 12 (Bookworm) / science / paleomix

Package: paleomix

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [geogenetics.ku.dk]

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

No published records match this suite and architecture filter.

Package file paths (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-1.3.7.egg-info/dependency_links.txt
/usr/lib/python3/dist-packages/paleomix-1.3.7.egg-info/entry_points.txt
/usr/lib/python3/dist-packages/paleomix-1.3.7.egg-info/not-zip-safe
/usr/lib/python3/dist-packages/paleomix-1.3.7.egg-info/PKG-INFO
/usr/lib/python3/dist-packages/paleomix-1.3.7.egg-info/requires.txt
/usr/lib/python3/dist-packages/paleomix-1.3.7.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
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/common.py
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/config.py
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/database.py
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/__init__.py
/usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/admixture.py
/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
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_02.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_03.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_04.fastq.gz
/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
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_03.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_04.fastq.gz
/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
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_02.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_03.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_01.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_02.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_03.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_01.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_02.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_03.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_01.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_02.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_03.fastq.gz
/usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/makefile.yaml
/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

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Versions, suites, and repositories

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Catalog record completeness

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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 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5, Debian 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00. The cross-OS mapping is catalog-derived from the source-reported homepage; it does not establish authorship or publisher identity

Sources and 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 12 (Bookworm) main amd64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
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/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
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: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Observed SHA-256: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Result: match verified
Debian 12 (Bookworm) main arm64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
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/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
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: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Observed SHA-256: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Result: match verified