NCBItax2lin

Convert NCBI taxonomy dump into lineages. An example for human (tax_id=9606) is like

| tax_id | superkingdom | phylum | class | order | family | genus | species | family1 | forma | genus1 | infraclass | infraorder | kingdom | no rank | no rank1 | no rank10 | no rank11 | no rank12 | no rank13 | no rank14 | no rank15 | no rank16 | no rank17 | no rank18 | no rank19 | no rank2 | no rank20 | no rank21 | no rank22 | no rank3 | no rank4 | no rank5 | no rank6 | no rank7 | no rank8 | no rank9 | parvorder | species group | species subgroup | species1 | subclass | subfamily | subgenus | subkingdom | suborder | subphylum | subspecies | subtribe | superclass | superfamily | superorder | superorder1 | superphylum | tribe | varietas | |--------|--------------|----------|----------|----------|-----------|-------|--------------|---------|-------|--------|------------|-------------|---------|--------------------|--------------|----------------------|-----------|-----------|-----------|-----------|---------------|-----------|-----------|-----------|-----------|-----------|-----------|-----------|-----------|-----------|---------------|------------|---------------|------------|--------------|---------------|------------|---------------|------------------|----------|----------|-----------|----------|------------|-------------|-----------|------------|----------|------------|-------------|------------------|-------------|-------------|-------|----------| | 9606 | Eukaryota | Chordata | Mammalia | Primates | Hominidae | Homo | Homo sapiens | | | | | Simiiformes | Metazoa | cellular organisms | Opisthokonta | Dipnotetrapodomorpha | Tetrapoda | Amniota | Theria | Eutheria | Boreoeutheria | | | | | Eumetazoa | | | | Bilateria | Deuterostomia | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Catarrhini | | | | | Homininae | | | Haplorrhini | Craniata | | | | Hominoidea | Euarchontoglires | | | | |

Install

ncbitax2lin supports python-3.9 to python-3.13.

pip install -U ncbitax2lin

It is also available in Conda on the Bioconda channel:

conda install bioconda::ncbitax2lin

Generate lineages

First download taxonomy dump from NCBI:

wget -N ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
mkdir -p taxdump && tar zxf taxdump.tar.gz -C ./taxdump

Then, run ncbitax2lin

ncbitax2lin --nodes-file taxdump/nodes.dmp --names-file taxdump/names.dmp

By default, the generated lineages will be saved to ncbi_lineages_[date_of_utcnow].csv.gz. The output file can be overwritten with --output option.

FAQ

Q: I have a large number of sequences with their corresponding accession numbers from NCBI, how to get their lineages?

A: First, you need to map accession numbers (GI is deprecated) to tax IDs based on nucl_*accession2taxid.gz files from ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/. Secondly, you can trace a sequence's whole lineage based on its tax ID. The tax-id-to-lineage mapping is what NCBItax2lin can generate for you.

If you have any question about this project, please feel free to create a new issue.

Note on taxdump.tar.gz.md5

It appears that NCBI periodically regenerates taxdump.tar.gz and taxdump.tar.gz.md5 even when its content is still the same. I am not sure how their regeneration works, but taxdump.tar.gz.md5 will differ simply because of a different timestamp.

Used in

• Mahmoudabadi, G., & Phillips, R. (2018). A comprehensive and quantitative exploration of thousands of viral genomes. ELife, 7. https://doi.org/10.7554/eLife.31955
• Dombrowski, N. et al. (2020) Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution, Nature Communications. Springer US, 11(1). doi: 10.1038/s41467-020-17408-w. https://www.nature.com/articles/s41467-020-17408-w
• Schenberger Santos, A. R. et al. (2020) NAD+ biosynthesis in bacteria is controlled by global carbon/ nitrogen levels via PII signaling, Journal of Biological Chemistry, 295(18), pp. 6165–6176. doi: 10.1074/jbc.RA120.012793. https://www.sciencedirect.com/science/article/pii/S0021925817482433
• Villada, J. C., Duran, M. F. and Lee, P. K. H. (2020) Interplay between Position-Dependent Codon Usage Bias and Hydrogen Bonding at the 5' End of ORFeomes, mSystems, 5(4), pp. 1–18. doi: 10.1128/msystems.00613-20. https://msystems.asm.org/content/5/4/e00613-20
• Byadgi, O. et al. (2020) Transcriptome analysis of amyloodinium ocellatum tomonts revealed basic information on the major potential virulence factors, Genes, 11(11), pp. 1–12. doi: 10.3390/genes11111252. https://www.mdpi.com/2073-4425/11/11/1252
• Cumbo, F., & Blankenberg, D. (2025). Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees. bioRxiv. https://doi.org/10.1101/2025.08.25.672238

Development

Install dependencies

poetry install --sync

Testing

make format
make all

Publish (only for administrator)

poetry version [minor/major etc.]
git tag vx.y.z
git push origin vx.y.z
poetry publish --build -u __token__ --password pypi-<token-from-pypi>

Update CHANGELOG.md.