<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · Taxonomy.jl</title><meta name="title" content="Home · Taxonomy.jl"/><meta property="og:title" content="Home · Taxonomy.jl"/><meta property="twitter:title" content="Home · Taxonomy.jl"/><meta name="description" content="Documentation for Taxonomy.jl."/><meta property="og:description" content="Documentation for Taxonomy.jl."/><meta property="twitter:description" content="Documentation for Taxonomy.jl."/><meta property="og:url" content="https://banhbio.github.io/Taxonomy.jl/"/><meta property="twitter:url" content="https://banhbio.github.io/Taxonomy.jl/"/><link rel="canonical" href="https://banhbio.github.io/Taxonomy.jl/"/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link 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class="docs-heading-anchor" href="#Taxonomy.jl">Taxonomy.jl</a><a id="Taxonomy.jl-1"></a><a class="docs-heading-anchor-permalink" href="#Taxonomy.jl" title="Permalink"></a></h1><p><a href="https://banhbio.github.io/Taxonomy.jl/dev"><img src="https://img.shields.io/badge/docs-dev-blue.svg" alt="Dev"/></a></p><p><a href="https://github.com/banhbio/Taxonomy.jl/actions/workflows/ci.yml"><img src="https://github.com/banhbio/Taxonomy.jl/actions/workflows/ci.yml/badge.svg" alt="CI"/></a> <a href="https://codecov.io/gh/banhbio/Taxonomy.jl"><img src="https://codecov.io/gh/banhbio/Taxonomy.jl/branch/main/graph/badge.svg?token=2A8WQRHRLC" alt="codecov"/></a></p><p><a href="https://zenodo.org/badge/latestdoi/341212699"><img src="https://zenodo.org/badge/341212699.svg" alt="DOI"/></a></p><h2 id="v0.5.0-Release-Notes"><a class="docs-heading-anchor" href="#v0.5.0-Release-Notes">v0.5.0 Release Notes</a><a id="v0.5.0-Release-Notes-1"></a><a class="docs-heading-anchor-permalink" href="#v0.5.0-Release-Notes" title="Permalink"></a></h2><h3 id="Breaking-changes"><a class="docs-heading-anchor" href="#Breaking-changes">Breaking changes</a><a id="Breaking-changes-1"></a><a class="docs-heading-anchor-permalink" href="#Breaking-changes" title="Permalink"></a></h3><ul><li><code>reformat</code> now accepts only canonical rank symbols.</li><li><code>reformat</code> now throws <code>UnCanonicalRankError</code> for non-canonical ranks and <code>RankAliasError</code> when multiple aliases for the same rank slot are requested.</li><li><code>:domain</code>, <code>:superkingdom</code>, and <code>:realm</code> are treated as aliases for the same top-rank slot.</li><li>Removed the <code>DataAPI</code> dependency. <code>All</code>, <code>Cols</code>, <code>Between</code>, <code>From</code>, and <code>Until</code> are now Taxonomy.jl selectors.</li><li>Removed support for <code>All(args...)</code>; use <code>Cols(args...)</code> for selecting multiple lineage positions or ranks.</li></ul><h3 id="Improvements"><a class="docs-heading-anchor" href="#Improvements">Improvements</a><a id="Improvements-1"></a><a class="docs-heading-anchor-permalink" href="#Improvements" title="Permalink"></a></h3><ul><li><code>name2taxids</code> now uses a per-<code>DB</code> lazy cache, fixing behavior when multiple taxonomy databases are used.</li><li><code>children(taxon)</code> now uses a per-<code>DB</code> lazy child index for faster parent-to-child traversal.</li><li><code>lca</code> now handles edge cases explicitly: empty input throws <code>ArgumentError</code>, and single-taxon input returns that taxon.</li><li>Database imports now use size-hinted vectors instead of fixed-size buffers.</li></ul><h2 id="Overview"><a class="docs-heading-anchor" href="#Overview">Overview</a><a id="Overview-1"></a><a class="docs-heading-anchor-permalink" href="#Overview" title="Permalink"></a></h2><p>Taxonomy.jl is a Julia package to handle the NCBI Taxonomy database. The main features are:</p><ul><li>Get various information on a given taxon (name, rank, parent-child relationships, etc.)</li><li>Convert a name to taxids</li><li>Traverse taxonomic subtrees from a given taxon</li><li>Compute the lowest common ancestor (LCA) of given taxa</li><li>Evaluate ancestor-descendant relationships between two taxa</li><li>Filter taxa by a rank range</li><li>Construct the taxonomic lineage of a given taxon</li><li>Reformat lineage according to canonical ranks</li><li>Construct a <code>DataFrame</code> from lineages</li></ul><p>Currently, this package only supports <code>scientific name</code>.</p><h2 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h2><p>Install Taxonomy.jl as follows:</p><pre><code class="nohighlight hljs">julia -e 'using Pkg; Pkg.add("Taxonomy")'</code></pre><h2 id="Download-the-database"><a class="docs-heading-anchor" href="#Download-the-database">Download the database</a><a id="Download-the-database-1"></a><a class="docs-heading-anchor-permalink" href="#Download-the-database" title="Permalink"></a></h2><p>You need to download taxonomic data from NCBI's servers.</p><pre><code class="nohighlight hljs">wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
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