4Peaks is a free Mac application for opening, inspecting, and editing chromatogram files produced by DNA sequencing machines — the kind of trace data that comes back from a Sanger sequencing run.
What is 4Peaks?
4Peaks is a dedicated chromatogram viewer and editor for macOS that reads AB1, SCF, and related DNA sequence trace formats. If you have ever squinted at a raw sequencing result in a generic text editor, wondering which ambiguous base call to trust, 4Peaks is the tool that turns that frustration into a clean, colour-coded trace you can actually reason about. It was built by Nucleobytes specifically for molecular biologists who work with sequenced samples daily and need something faster and more legible than exporting to a spreadsheet.
I have used it to verify primer alignments, manually correct automated base calls, and export clean FASTA sequences for downstream cloning work. It is one of those niche utilities that, once you discover it, becomes impossible to work without.
What does 4Peaks do best?
4Peaks excels at rendering the four-channel fluorescence trace in a crisp, zoomable interface where you can immediately see which peaks are clean and which are noisy or overlapping. The colour coding — one colour per nucleotide base — is clear even on small displays, and the zoom level can be adjusted smoothly so you can inspect a suspicious region at single-base resolution.
- Manual base-call editing: Click any base in the sequence and change it. The edited call updates inline without touching the underlying trace data.
- Quality score display: Phred scores are overlaid directly on the trace, so you know at a glance which automated calls are confident and which are guesses.
- FASTA and text export: Copy a clean sequence to the clipboard or export to FASTA for immediate use in BLAST, SnapGene, or any alignment tool.
- Batch opening: Drop a folder of AB1 files onto the Dock icon and work through them in a tabbed window — essential when a plate of 96 samples comes back from the sequencing facility.
- Primer trimming view: The app can highlight low-quality end regions so you know exactly where to truncate before submitting a sequence.
Compared to the web-based Benchling chromatogram viewer or the Java-heavy Chromas on Windows, 4Peaks loads in a fraction of a second and feels genuinely native on macOS — scrolling is butter-smooth and keyboard shortcuts work the way you expect.
Is 4Peaks free?
Yes — 4Peaks is free to download and use with no time limits, feature paywalls, or registration required. Nucleobytes has kept it freely available for the research community for many years, which is remarkable given how polished it is. There is no subscription, no premium tier, and no nag screen. If you want to support the developer, the website has a donation link, and I would encourage any lab that relies on it to consider contributing.
Who should use 4Peaks?
4Peaks is the right tool for anyone doing Sanger sequencing on a Mac — molecular biologists, graduate students, clinical lab technicians, or bioinformaticians who need a quick sanity-check before handing a sequence off to a pipeline. It is not a full sequence analysis suite; for multiple-sequence alignment or primer design you would still reach for Geneious, SnapGene, or even the free UGENE. But for the specific job of reviewing and lightly editing a chromatogram trace, nothing on the Mac platform touches it.
If your lab is still emailing AB1 files to a Windows machine just to open them in Chromas, 4Peaks eliminates that entirely.
How does 4Peaks compare to Geneious?
Geneious (now Geneious Prime) is a comprehensive molecular biology workbench that does assembly, annotation, phylogenetics, and a great deal more — at a subscription price that starts in the hundreds of dollars per year. 4Peaks does exactly one thing — chromatogram viewing and editing — and does it for free. The two tools are not really competing; most researchers I know run both. Open your trace in 4Peaks for a fast visual check and manual correction, then import the final sequence into Geneious or SnapGene for assembly or annotation work. UGENE is the closest free alternative for the full-suite use case, but its chromatogram viewer is noticeably less refined than 4Peaks on Mac.
What are the best 4Peaks alternatives?
If 4Peaks does not meet your needs, the next options worth considering are:
- Chromas (Windows only, free) — the closest equivalent on Windows; no Mac version.
- Geneious Prime (Mac/Win/Linux, paid) — includes a chromatogram viewer but costs significantly more.
- SnapGene Viewer (free) — excellent for plasmid maps; chromatogram support is secondary.
- UGENE (free, open source) — cross-platform, feature-rich, but heavier and less polished on macOS.
- Benchling (browser-based, free for academics) — handles traces in the browser, useful if you need cloud storage and sharing.
For pure, fast, offline trace viewing on a Mac, none of those alternatives match 4Peaks on speed or ease of use.
