ncbi-tree

ncbi-tree is an open source, cross-platform command-line tool for downloading the latest NCBI taxonomy database and converting it to Newick tree format (.tre), with optional plain-text visualization (.txt).

Quick Start

pip install ncbi-tree
ncbi-tree ./output

That's it! The tool will download the latest NCBI taxonomy, generate phylogenetic trees, and create detailed reports.

Features

• Automatic Download: Fetches the latest taxonomy data from NCBI FTP servers
• Version Tracking: Automatically detects and records the exact server version
• Smart Caching: Skips re-download and re-extraction when files already exist
• Merged Taxa Support: Handles merged taxonomy IDs from merged.dmp
• Name Sanitization: By default inital letter is capitalized and space is replaced by -. Configurable name formatting with --no-sanitize option
• Server-side compatibility: No more blocking on user input in automated environments. Use ncbi-tree ./output --no-prompt-1 to automatically generate all files (core + optional); Use ncbi-tree ./output --no-prompt-0 to generate only core files, skip optional files.

Installation

pip install ncbi-tree

Usage

Basic Usage

# Download and build taxonomy tree with default settings
ncbi-tree ./output

# Clean up intermediate files after processing
ncbi-tree ./output --no-cache

# Disable name sanitization (keep original spaces)
ncbi-tree ./output --no-sanitize

# Use custom download URL
ncbi-tree ./output --url https://custom-mirror.org/taxdump.tar.gz

# Combined options
ncbi-tree ./output --no-cache --no-sanitize

Server-side, non-blocking, no-interaction

# Automatically generate all files (core + optional)
ncbi-tree ./output --no-prompt-1

# Generate only core files, skip optional files
ncbi-tree ./output --no-prompt-0

Help

ncbi-tree --help
ncbi-tree --version

Output Files

Core Files (Generated Automatically)

1. output.NCBI.tree.tre - Newick tree with NCBI taxonomy IDs only
2. output.NCBI.report.txt - Exploratory taxonomy analysis and statistics
3. version.txt - Server timestamped version for downloaded taxdump.tar.gz

Optional Files (User Prompted)

After core files are generated, you will be prompted:

Would you like to generate optional files (output.NCBI.tree.txt, output.NCBI.named.tree.tre, output.NCBI.ID.to.name.tsv)? [y/N]:

If you answer y, additional files will be generated without re-reading data:

4. output.NCBI.tree.txt - Plain-text tree with Unicode box-drawing
5. output.NCBI.named.tree.tre - Newick tree with rank:id:name labels
6. output.NCBI.ID.to.name.tsv - TSV mapping of IDs to names (TaxID, Name, Rank)

Name Sanitization

By default, taxon names are sanitized for consistent display:

• Spaces replaced with -
• Existing - escaped as <->, which will be eventually escaped back to -. Configurable by changing name = name.replace('-', '<->') in sanitize_name in core.py.
• Title case applied
• Special characters removed

Default (sanitized):

"Human;Homo-Sapiens"
"Norway-Rat;Rattus-Norvegicus"

With --no-sanitize flag:

"human; Homo sapiens"
"Norway rat; Rattus norvegicus"

Advanced Configuration

Custom Name Display

To customize which name types are displayed, edit NAME_PRIORITIES in ncbi_tree/core.py:

# Default: both common and scientific names
NAME_PRIORITIES = {"genbank common name": 0, "scientific name": 1}
# Result: "Human; Homo sapiens"

# Scientific name only (disable common name)
NAME_PRIORITIES = {"genbank common name": -1, "scientific name": 0}
# Result: "Homo sapiens"

# Common name only (disable scientific name)
NAME_PRIORITIES = {"genbank common name": 0, "scientific name": -1}
# Result: "Human"

Note: Priority value -1 disables that name type, >= 0 enables it (lower number = higher priority).

Requirements

• Python 3.8 or higher
• requests >= 2.25.0
• tqdm >= 4.50.0

Technical Details

Data Source

• Primary: NCBI Taxonomy Database (https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/)
• Updates: Automatic detection of latest version with timestamp tracking
• Size: ~70-100 MB compressed, ~2.7M+ taxonomy entries at the time of writing (October 2025)
• Format: NCBI taxdump format (nodes.dmp, names.dmp, merged.dmp)

Output Formats

1. Newick (.tre): Standard phylogenetic tree format compatible with all major tree viewers
2. Text Tree (.txt): Unicode-based visualization for terminal/text viewing
3. TSV Mapping (.tsv): Tabular format for database integration and lookups
4. Report (.txt): Statistical analysis with rank distribution and depth metrics

License

This project is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).

Contributing

Contributions are welcome! Please feel free to submit issues or pull requests.

Acknowledgments

• Schoch CL, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020: baaa062. PubMed
• Sayers EW, et al. GenBank. Nucleic Acids Res. 2019. 47(D1):D94-D99. PubMed