This is a Next.js project bootstrapped with create-next-app.

Getting Started

First, run the development server:

npm run dev
# or
yarn dev
# or
pnpm dev
# or
bun dev

Open http://localhost:3000 with your browser to see the result.

You can start editing the page by modifying app/page.tsx. The page auto-updates as you edit the file.

This project uses next/font to automatically optimize and load Geist, a new font family for Vercel.

Learn More

To learn more about Next.js, take a look at the following resources:

• Next.js Documentation - learn about Next.js features and API.
• Learn Next.js - an interactive Next.js tutorial.

You can check out the Next.js GitHub repository - your feedback and contributions are welcome!

Deploy on Vercel

The easiest way to deploy your Next.js app is to use the Vercel Platform from the creators of Next.js.

Check out our Next.js deployment documentation for more details.

Analytics (Google Analytics 4)

This project supports GA4 to track visits and geography.

1. Create a GA4 property and web data stream. Copy the Measurement ID (looks like G-XXXXXXX).

2. Set the environment variable locally or in your hosting provider:

NEXT_PUBLIC_GA_MEASUREMENT_ID=G-XXXXXXX

You can use .env.local during development. See .env.local.example.

3. The app automatically loads GA and tracks route changes. No additional setup is needed.

Notes:

• GA4 reports: Acquisition (source/medium/referrals) and Demographics (country/city).
• GA4 does not identify individual users; data is aggregate. Ensure cookie/consent compliance as required.

Phyletic-distribution taxonomy tree

Generate the NCBI Taxonomy hierarchy used by the hidden phyletic-distribution tool:

npm run generate:phyletic-tree

The taxonomy covers every organism in the searched database, the 2,760 NCBI taxIDs of the UniProt 2025_02 eukaryotic reference proteome set, including organisms in which no family was found (a taxon with no counts row has no hits in any family). taxonomy_eukaryotes_filtered.json is built from that taxID list with scripts/ncbi_taxonomy_create.py and the NCBI taxonomy dump of September 2025. TaxID 1450536, since merged by NCBI into 856835 (Guyanagaster necrorhizus), is placed at 856835 and keeps its searched ID.

The page can switch to the Open Tree of Life reference taxonomy (OTT 3.7.3), served as taxonomy_ott.json, taxonomy_ott.nwk and taxonomy_ott.tree-order.json in the same formats. It is matched to the same taxIDs through OTT's ncbi: source identifiers and places 2,662 of the 2,760; the 98 OTT has no NCBI mapping for are absent from that view. The OTT files are not made by generate:phyletic-tree: OTT's rank labels do not nest (an unranked group can sit above a larger "order"), so rebuilding the nesting from flat rank columns fails, and the newick is written from the OTT hierarchy itself with internal nodes labelled rank__name like the NCBI tree. Both sets of files are built by build_taxonomy_trees.py in the GPCR superfamily analysis (step 7).

The generator reads public/phyletic-distribution/taxonomy_eukaryotes_filtered.json and writes public/phyletic-distribution/taxonomy_eukaryotes_filtered.nwk plus public/phyletic-distribution/taxonomy_eukaryotes_filtered.tree-order.json.

• Newick tips are NCBI taxIDs so they map directly to visualization records.
• Every populated taxonomy field is retained, including Cellular Root, all named ranks, Clade through Clade 21, and No Rank through No Rank 3. Empty and NA values never create nodes.
• Because the JSON stores ranked and unranked fields in separate flattened columns, groups are nested by containment of their sampled descendant taxa. Repeated names in different lineages are separated by broader context.
• Multifurcations are preserved as nodes with any number of children; the tree is never forced into a binary topology.
• The companion order file is the authoritative leaf order used by the visualization, preventing the taxonomy bars and tree tips from diverging.
• Branch lengths are layout distances, not evolutionary distances. The whole hierarchy is stretched to the available height; lineages may contain different numbers of populated taxonomy layers while all tips stay aligned.

For future visualization, prune the tree by visible taxID tips and retain child arrays of arbitrary length. The NCBI tree should be described as a taxonomy hierarchy and displayed as a cladogram by default.