In 2025 MorphoBank rebuilt its underlying architecture from the ground up to deliver faster performance through an intuitive modern interface. Now, we’re layering new features and functionality over that stronger, modern foundation.
MorphoBank gets a makeover
MorphoBank got its start in 2001. By 2025, the system was due for an upgrade. It was built on PHP architecture meant for smaller datasets. As users added tens of thousands of images, matrices, and taxa to MorphoBank, it became harder to maintain and slower under heavy use.
Engineers at Phoenix Bioinformatics, the nonprofit organization that hosts MorphoBank, undertook a replatforming project designed to bring MorphoBank up-to-date. Funded by a grant from the National Science Foundation (NSF award EAR-2148768), they completely rebuilt the tool using modern open source technologies to deliver faster performance, an accessible, mobile-friendly user experience, and a more scalable database system. The replatforming work, completed and launched in Autumn 2025, included some new integrations, analysis, and features.
New analytical tool TNT
Among the most exciting updates made possible on our new platform is the addition of the Tree Analysis using New Technology (TNT), a widely used program for parsimony-based phylogenetic analysis. TNT provides advanced phylogenetic analysis capabilities, including:
- Implicit Enumeration: Guarantees finding the most parsimonious tree(s) for small datasets (≤30 taxa)
- Traditional Search: Standard approach for larger datasets with customizable parameters, it uses multiple random addition sequences and/or branch swapping, useful for medium numbers of taxa (20-80 taxa)
- New Technology Search: Combines several types of algorithms (ratchet, sectorial searches, drifting, and fusing), useful for larger data sets (i.e. above 150 taxa), and is much more effective than traditional searches.
This tool converts your matrix to TNT format and provides direct access to TNT algorithms for tree building and analysis. Results are returned as NEXUS files including the inferred tree(s) and relevant analysis output.
MorphoBank gratefully acknowledges Dr. Pablo Goloboff (CONICET – Fundación Miguel Lillo, Argentina) for granting permission to include the TNT algorithm in the platform.
More integrations and updates
ORCID integration for dataset credit. Link your ORCID iD to your MorphoBank account to streamline your CV process. Opt-in to have MorphoBank projects automatically added to your ORCID profile upon publication, helping make your data contributions more visible, citable, and connected to your broader research output. Plus, simplify sign-in using your ORCID credentials.
Combine specimens with ease. Our new composite taxon/OTU tool allows researchers to combine multiple taxa rows into a single composite row with merged scores, streamlining the process of combining multiple specimens from the same species into the record.
Upload Excel and CSV files. If you captured your original data in these file formats, you can now upload them into the database.
- For continuous data: your matrix must have taxa as rows and characters as columns, with character names as the first row.
- For discrete data: your matrix must have taxa as rows and characters as columns, with character names in Row 1 and character states in Row 2 for each matched character column.
- Mixed continuous and discrete character CSV or Excel files are currently NOT handled.
Extract data from NEXUS and TNT files. Now, you can upload NEXUS or TNT files even if they don’t have the character names and states included. Give our software the PDF or .docx file with character information and our integrated AI-data extractor will identify the relevant data and add it to the matrices.
We’re not done yet
Now that the grant funding has concluded, the Phoenix Bioinformatics technical team aims to continue expanding matrix creation and editing options as future funding allows, including adding support for more data formats and improving scoring efficiency.
Your support is critical to future development and maintenance. MorphoBank is open source, free-to-use, and predominantly Open Access. That’s only possible because of the support of our member libraries and museums. Contact us to learn more about membership.
