https://github.com/banhbio/taxonomy.jl

Julia package to handle the NCBI Taxonomy database.
https://github.com/banhbio/taxonomy.jl

biodiversity bioinformatics julia ncbi ncbi-database ncbi-taxonomy phylogeny taxonomy

Last synced: about 2 months ago
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Julia package to handle the NCBI Taxonomy database.

• Host: GitHub
• URL: https://github.com/banhbio/taxonomy.jl
• Owner: banhbio
• License: mit
• Created: 2021-02-22T13:39:11.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2025-03-11T06:53:20.000Z (7 months ago)
• Last Synced: 2025-06-11T12:26:34.164Z (4 months ago)
• Topics: biodiversity, bioinformatics, julia, ncbi, ncbi-database, ncbi-taxonomy, phylogeny, taxonomy
• Language: Julia
• Homepage:
• Size: 545 KB
• Stars: 13
• Watchers: 1
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# Taxonomy.jl

[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://banhbio.github.io/Taxonomy.jl/dev)

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[![codecov](https://codecov.io/gh/banhbio/Taxonomy.jl/branch/main/graph/badge.svg?token=2A8WQRHRLC)](https://codecov.io/gh/banhbio/Taxonomy.jl)

[![DOI](https://zenodo.org/badge/341212699.svg)](https://zenodo.org/badge/latestdoi/341212699)

Taxonomy.jl is a julia package to handle the NCBI Taxonomy database.

The main features are:

- Get various information on a given taxon (name, rank, parent-child relationships, etc.)

- Convert a name to Taxids

- Traverse taxonomic subtrees from a given taxon

- Compute the lowest common ancestor (LCA) of given taxa

- Evaluate ancestor-descendant relationships between two taxa

- Filter taxa by a rank range

- Construct taxonomic lineage of the given taxon

- Reformat lineage according to canonical ranks

- Construct a `DataFrame` from lineages

Now, this package only supports `scientific name`.

## Installation

Install Taxonomy.jl as follows:

```

julia -e 'using Pkg; Pkg.add("Taxonomy")'

```

## Download database

You need to download taxonomic data from NCBI's servers.

```

wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz

tar xzvf taxdump.tar.gz

```