BioNumerics and GelCompar II Alternative for Gel Fingerprinting and Dendrograms

For two decades, microbiology and plant genetics labs turned banding patterns into dendrograms in GelCompar II or BioNumerics. Applied Maths has now discontinued GelCompar II and announced the phase-out of BioNumerics, so labs that still type strains by RAPD, ERIC-PCR, PFGE, DGGE or RFLP need somewhere to take their gels. CLIQS 1D Pro from TotalLab does that job: automatic band matching across gels, UPGMA dendrograms with Dice or Jaccard similarity, and a reference library for classifying new isolates. No 0/1 scoring in a spreadsheet.

What happened to GelCompar II and BioNumerics

GelCompar II was Applied Maths’ software for comparing electrophoresis fingerprints. Applied Maths announced its discontinuation after 25 years, citing the move of epidemiology toward whole genome sequencing. Existing licenses keep working, but maintenance and support stopped, and GelCompar II users were offered a discounted move to BioNumerics until 31 December 2018 [1].

BioNumerics, the larger platform that also handled gel fingerprints, followed. Applied Maths, part of bioMérieux since 2016, announced in October 2021 that BioNumerics would be phased out by the end of 2024.

For a lab that still runs gels, this leaves three problems. Licenses tied to a dongle cannot be replaced when hardware fails. Windows updates are not tested against unsupported software. And a database of historical fingerprints has no maintained software to add new isolates to.

What labs are using instead

The recent literature shows where fingerprinting labs went. Some moved to GelJ, a free Java tool, to build UPGMA dendrograms with the Dice coefficient; a 2025 study of Pseudomonas aeruginosa from trout farms is a typical example [4]. Others score bands by hand as present or absent in a spreadsheet and cluster the matrix in PAST, NTSYS or R.

Both routes work for a small study. They get harder as the number of gels grows: band positions shift from gel to gel, manual 0/1 scoring depends on who does it, and nothing links the dendrogram back to the gel images a reviewer or auditor may ask to see.

How to build a dendrogram from 1D gel band patterns

Moving your fingerprint workflow to CLIQS 1D Pro

CLIQS 1D Pro is built for comparing banding patterns across many gels. The workflow will look familiar to anyone who used GelCompar II in the past:

• Import your analyzed gel images. CLIQS 1D Pro opens TIFF image files analysed in our CLIQS software, so the original images behind an old GelCompar II or BioNumerics database can be re-analyzed.
• CLIQS performs all the features you’d expect to prepare your images – Automatic lane and band detection, background subtraction, and molecular size is calculated from your ladder by curve fitting.
• Accurately normalize between different gels. Rf calibration corrects for gels that ran differently, so the same fragment lines up across the whole study.
• Match bands. Bands are matched across lanes and gels within a tolerance window you set. The band-sharing result is the Dice similarity: twice the matched bands divided by the total bands in both lanes.
• Cluster and classify. CLIQS 1D Pro builds an interactive UPGMA dendrogram with Dice or Jaccard similarity and a similarity matrix, and classifies unknown isolates against a reference library of known strains that you maintain.
• Report. Export annotated images, cluster tables and similarity matrices to PDF and Excel.
• For regulated labs, CLIQS 1D Pro works with AuditSafe, which adds audit trails, electronic signatures and granular user permissions for FDA 21 CFR Part 11 and EU Annex 11.

See CLIQS 1D Pro

Feature comparison for gel fingerprinting

This table compares the gel fingerprinting tasks, not the whole of each product. BioNumerics also covered sequence and whole genome analysis, which CLIQS 1D Pro does not. In short, all four packages do the core fingerprinting the same way. Each detects bands automatically, normalizes between gels using Rf, matches bands within a set tolerance, and builds UPGMA dendrograms from Dice or Jaccard similarity. The differences sit around the analysis rather than in it. GelCompar II is discontinued and its support has ended, BioNumerics is being phased out, and GelJ is free and open-source with community support only and no 21 CFR Part 11 audit trail or electronic signatures. CLIQS 1D Pro is actively developed and supported, classifies unknown samples against a reference library, adds 21 CFR Part 11 audit trails and electronic signatures through AuditSafe, and comes with a fully functional free trial.

Gel fingerprinting options after the GelCompar II and BioNumerics phase-out. Status as announced by the developers; see references

How to report it in your methods

Reviewers expect the software, the clustering method, the similarity coefficient and the tolerance. This sentence covers all four:

“Banding patterns were analyzed in CLIQS 1D Pro (TotalLab Ltd, Newcastle upon Tyne, UK). A dendrogram was constructed by UPGMA using the Dice similarity coefficient with a [X]% band position tolerance.”

Frequently Asked Questions

Is GelCompar II still supported?

No. Applied Maths discontinued GelCompar II and stopped maintenance and support. Existing licenses can still be used, but there are no further updates [1].

Is BioNumerics being discontinued?

Yes. Applied Maths announced in October 2021 that BioNumerics would be phased out by the end of 2024 [2][3].

What is the best BioNumerics alternative for RAPD, ERIC-PCR or PFGE dendrograms?

If your data is gel images, CLIQS 1D Pro covers the same fingerprint workflow: automatic band matching across gels, Rf calibration, UPGMA dendrograms with Dice or Jaccard similarity, and classification against a reference library. If your lab has moved to whole genome sequencing, you need a sequence analysis platform instead.

Can I use GelJ instead?

GelJ is free and builds UPGMA dendrograms from gel images, and many papers use it. Labs choose CLIQS 1D Pro when they need a database that grows across many gels, a reference library for classifying new isolates, vendor support, or 21 CFR Part 11 controls through AuditSafe.

Which techniques does CLIQS 1D Pro support?

DNA fingerprinting, PFGE, RAPD, ERIC-PCR, DGGE, RFLP, AFLP, SSCP, ARISA-PCR, ISSR-PCR, microsatellites and minisatellites, and lateral flow assays.

Which similarity coefficients and clustering methods does it use?

Dice or Jaccard similarity, clustered by UPGMA.

Is CLIQS 1D Pro compatible with PulseNet work?

TotalLab describes CLIQS 1D Pro as fully compatible with the work done at PulseNet International for tracking food and waterborne disease outbreaks.

How many lanes can a database hold?

The number of lanes is limited only by memory and disk space, and databases have been tested with more than 500 lanes. Several users can open a database at the same time.

Can I try it on my own gels?

Yes. The free trial is fully functional, and TotalLab can run an online demonstration with your images.

References

[1] Applied Maths. Attention all GelCompar II users. https://www.applied-maths.com/news/attention-all-gelcompar-ii-users
(Source for: GelCompar II discontinuation, end of maintenance and support, migration offer to 31-12-2018)

[2] Applied Maths. BIONUMERICS phasing out. https://www.applied-maths.com/bionumerics/category/bionumerics-phasing-out
(Source for: BioNumerics phase-out)

[3] Wikipedia. Applied Maths. https://en.wikipedia.org/wiki/Applied_Maths
(Source for: October 2021 announcement, phase-out by end of 2024)

[4] Taha ZM. Random amplified polymorphic DNA polymerase chain reaction was used to analyze the genotype and diversity of Pseudomonas aeruginosa isolated from salmon trout farms with hemorrhagic septicemia. Open Vet J. 2025;15(8):3780-3786. doi:10.5455/OVJ.2025.v15.i8.42
(Source for: GelJ used to build a UPGMA dendrogram from RAPD-PCR fingerprints)

[5] TotalLab. CLIQS 1D Pro product page. https://totallab.com/software/1d-gel-electrophoresis-band-matching-software/
(Source for: all CLIQS 1D Pro features, formats, techniques, PulseNet statement and methods sentence)

Bring your gels. Keep your dendrograms.

Try CLIQS 1D Pro free on your own RAPD, ERIC-PCR or PFGE images, or book a demo and we will run your gels with you.

Talk to us: +44 191 255 8899 or info@totallab.com