paleomix (1.3.10-1)
Details
Core information at a glance
- Distribution
- ubuntu
- Origin
- ubuntu-stonking
- Repository
- https://nl.archive.ubuntu.com/ubuntu
- Codename
- stonking
- Component
- universe
- Source
- none
- Architecture
- amd64
- Section
- universe/science
- Priority
- optional
- Maintainer
- Ubuntu Developers <[email protected]>
Size & integrity
Byte sizes and integrity verification
- Installed size
- 2 kB
- Size expected
- 971.2 kB
- Size actual
- 971.2 kB
- Size match
Dependencies
Required package dependencies
Suggested packages
Recommended additional packages
- None
Description
pipelines and tools for the processing of ancient and modern HTS data
Tags
Package classification tags
None
Checksums
Hash values and integrity verification status
| Type | Actual | Match |
|---|---|---|
| MD5 | 66f37337…317b8574 | |
| SHA-1 | c704149d…c8cfdfbb | |
| SHA-256 | 3df4270f…9b73c9f6 | |
| SHA-512 | 97145d5b…d2c020d2 |
Contents
Files and directories included
. usr usr/bin usr/bin/paleomix usr/lib usr/lib/python3 usr/lib/python3/dist-packages usr/lib/python3/dist-packages/paleomix usr/lib/python3/dist-packages/paleomix/__init__.py usr/lib/python3/dist-packages/paleomix/atomiccmd usr/lib/python3/dist-packages/paleomix/atomiccmd/__init__.py 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/pprint.py usr/lib/python3/dist-packages/paleomix/atomiccmd/sets.py usr/lib/python3/dist-packages/paleomix/common usr/lib/python3/dist-packages/paleomix/common/__init__.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 usr/lib/python3/dist-packages/paleomix/common/formats/__init__.py usr/lib/python3/dist-packages/paleomix/common/formats/_common.py usr/lib/python3/dist-packages/paleomix/common/formats/_graph.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/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/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/resources.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/main.py usr/lib/python3/dist-packages/paleomix/node.py usr/lib/python3/dist-packages/paleomix/nodegraph.py usr/lib/python3/dist-packages/paleomix/nodes usr/lib/python3/dist-packages/paleomix/nodes/__init__.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/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 usr/lib/python3/dist-packages/paleomix/pipelines/__init__.py usr/lib/python3/dist-packages/paleomix/pipelines/bam usr/lib/python3/dist-packages/paleomix/pipelines/bam/__init__.py usr/lib/python3/dist-packages/paleomix/pipelines/bam/config.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 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/phylo usr/lib/python3/dist-packages/paleomix/pipelines/phylo/__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/makefile.py usr/lib/python3/dist-packages/paleomix/pipelines/phylo/mkfile.py usr/lib/python3/dist-packages/paleomix/pipelines/phylo/parts usr/lib/python3/dist-packages/paleomix/pipelines/phylo/parts/__init__.py usr/lib/python3/dist-packages/paleomix/pipelines/phylo/parts/genotype.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 usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/__init__.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/parts usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/__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/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 usr/lib/python3/dist-packages/paleomix/resources/__init__.py usr/lib/python3/dist-packages/paleomix/resources/examples usr/lib/python3/dist-packages/paleomix/resources/examples/__init__.py usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data 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 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 usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/prefixes/rCRS.fasta usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment 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 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 usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions 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/reports usr/lib/python3/dist-packages/paleomix/resources/reports/zonkey usr/lib/python3/dist-packages/paleomix/resources/reports/zonkey/report.css usr/lib/python3/dist-packages/paleomix/resources/rscripts usr/lib/python3/dist-packages/paleomix/resources/rscripts/common usr/lib/python3/dist-packages/paleomix/resources/rscripts/common/requires.r usr/lib/python3/dist-packages/paleomix/resources/rscripts/zonkey 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 usr/lib/python3/dist-packages/paleomix/tools/__init__.py usr/lib/python3/dist-packages/paleomix/tools/bam_stats usr/lib/python3/dist-packages/paleomix/tools/bam_stats/__init__.py 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/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/rmdup_collapsed.py usr/lib/python3/dist-packages/paleomix/tools/rscript.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/lib/python3/dist-packages/paleomix-1.3.10.egg-info usr/lib/python3/dist-packages/paleomix-1.3.10.egg-info/PKG-INFO usr/lib/python3/dist-packages/paleomix-1.3.10.egg-info/dependency_links.txt usr/lib/python3/dist-packages/paleomix-1.3.10.egg-info/entry_points.txt usr/lib/python3/dist-packages/paleomix-1.3.10.egg-info/not-zip-safe usr/lib/python3/dist-packages/paleomix-1.3.10.egg-info/requires.txt usr/lib/python3/dist-packages/paleomix-1.3.10.egg-info/top_level.txt usr/share usr/share/doc usr/share/doc/paleomix usr/share/doc/paleomix/README.rst usr/share/doc/paleomix/README.test usr/share/doc/paleomix/changelog.Debian.gz usr/share/doc/paleomix/copyright usr/share/doc/paleomix/run-unit-test usr/share/doc/paleomix/tests usr/share/doc/paleomix/tests/README.rst usr/share/doc/paleomix/tests/atomiccmd_test usr/share/doc/paleomix/tests/atomiccmd_test/__init__.py 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/pprint_test.py.gz usr/share/doc/paleomix/tests/atomiccmd_test/sets_test.py.gz usr/share/doc/paleomix/tests/common_tests usr/share/doc/paleomix/tests/common_tests/__init__.py usr/share/doc/paleomix/tests/common_tests/bedtools_test.py.gz usr/share/doc/paleomix/tests/common_tests/formats_tests usr/share/doc/paleomix/tests/common_tests/formats_tests/__init__.py 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/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/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 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/node_test.py.gz usr/share/doc/paleomix/tests/nodegraph_test.py.gz usr/share/doc/paleomix/tests/tools_test usr/share/doc/paleomix/tests/tools_test/factory_test.py usr/share/lintian usr/share/lintian/overrides usr/share/lintian/overrides/paleomix usr/share/man usr/share/man/man1 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