Developer: M. Wayne Davis (University of Utah / Howard Hughes Medical Institute)
Supported platforms: Windows, macOS, and Linux (Tcl/Tk; v3.1.10.1, August 2026)
Download: https://jorgensen.biology.utah.edu/wayned/ape/
Features
View Quality scores
Yes. The chromatogram window includes a Toggle Phred control to show or hide the quality-score graph.
View raw data
No unprocessed capillary channel sweep view, though hovering over aligned bases in the alignment window brings up a live semi-opaque pop-up showing underlying chromatogram trace peaks and centred codon translations.
Assembly
No full de novo contig assembler, though ApE performs fast pairwise and multi-read alignment against reference plasmids or trace sequences (seed-and-extend plus Needleman-Wunsch global alignment).
Input file formats
.ab1, .scf, .ape, GenBank (.gb, .gbk), FASTA, EMBL, GCG, GFF3, pDraw, DNA Strider, Serial Cloner, Gene Construction Kit (.gck), and plain ASCII sequence text.
Output file formats
SCF 3.0 chromatogram export (Export as SCF), human-readable GenBank-compatible .ape files (which can embed linked .ab1 traces directly), standard GenBank, FASTA, PDF trace prints, Illustrator/Inkscape vector maps, and .pptx slide graphics.
Trimming
Yes. Alignment settings include configurable Phred-based end trimming, alongside manual sequence editing.
Integrated Blast
Yes. Direct NCBI BLAST (Tools > BLAST Sequences At NCBI...) and NCBI Entrez database retrieval.
Open multiple windows
Yes, including side-by-side sequence editor, chromatogram, graphic map, and alignment windows.
Edit bases
Yes, in the sequence and alignment windows.
ABI limits (regions outside of clear range region are displayed in gray)
Import and display of instrument ABI clear-range tags is not confirmed; ApE provides its own Phred-based end trimming and alignment views.
Other functions
- Auto-annotation against built-in and customisable feature libraries
- In silico cloning (restriction/ligation, Gibson, Golden Gate, Gateway/recombinase, and PCR)
- Restriction mapping (with Dam/Dcm methylation awareness), ORF finding, and dCAPS SNP primer design
Cost
Free (donation-supported; published in Frontiers in Bioinformatics).
Comments
ApE has remained a laboratory favourite for over two decades because it is fast, open-format, completely free on Windows, macOS, and Linux, and actively maintained. While it is not a high-throughput Phred/Phrap contig assembler, its hover-to-inspect chromatogram pop-ups during plasmid-to-read alignments and ability to embed .ab1 files inside .ape records make routine clone verification straightforward.
Return to the Trace Viewers overview or check trace quality online with QualTrace III Online.