Tools

• CD-HIT in Google Colab October 2026

  The CD-HIT web server has been unavailable since 2022, which left many users without an easy way to cluster sequences and remove redundancy. As an alternative, I wrote a Google Colab notebook that builds CD-HIT from source and runs it on your own sequences, entirely in the browser.

  All parameters are form fields with explanatory notes, so a saved copy of the notebook records exactly what was run. Each run also writes a provenance file with the CD-HIT version, the full command line, an input checksum and a timestamp. The notes also explain two options that are often confused, -s (minimum length ratio) and -aS (alignment coverage of the shorter sequence).

  Open in Colab · GitHub · Zenodo: 10.5281/zenodo.23503573

• EFI web tools (EFI-EST, EFI-GNT, EFI-CGFP) January 2019

  While part of the Enzyme Function Initiative team at the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, I helped build and improve the EFI-EST, EFI-GNT, and EFI-CGFP genomic enzymology web tools. This work is described across three papers with Nils Oberg and John Gerlt:

  • “The EFI web resource for genomic enzymology tools: leveraging protein, genome, and metagenome databases to discover novel enzymes and metabolic pathways”, Biochemistry, 2019
  • “Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools”, Current Opinion in Biotechnology, 2021
  • “EFI-EST, EFI-GNT, and EFI-CGFP: enzyme function initiative (EFI) web resource for genomic enzymology tools”, Journal of Molecular Biology, 2023

  I also run hands-on training workshops on the EFI tools, showing researchers how to build sequence similarity networks and explore genome context:

  • Institut Pasteur, Paris, 2019
  • University of Melbourne, Melbourne, 2023
  • National University of Singapore, Singapore, 2023
  • National Centre for Engineering Biology, National University of Singapore, Singapore, 2026
• Gene Graphics January 2018

  I built Gene Graphics, a web application for visualising genomic neighbourhoods, with Katherine Harrison and Valérie de Crécy-Lagard — described in “Gene Graphics: a genomic neighborhood data visualization web application” (Bioinformatics, 2018).