Developer: CodonCode Corporation
Supported platforms: Windows (64-bit) and macOS (including native Apple Silicon)
Download: https://www.codoncode.com/aligner/
Features
View Quality scores
Yes. Displays Phred/KB quality scores alongside base calls and uses quality-weighted consensus and discrepancy highlighting.
View raw data
Optional. Processed trace data is shown by default; raw ABI trace data can be retained via Preferences (commonly used for bisulfite methylation workflows).
Assembly
Yes. Full de novo and reference-guided Sanger contig assembly (using Phrap or built-in assemblers), batch “Assemble by name”, contig-to-contig alignment, and Clustal Omega / MUSCLE multiple sequence alignments.
Input file formats
.ab1, .abi, .scf, FASTA, FASTQ, SAM/BAM, GenBank, EMBL, PHD, GFF, and SnapGene .dna files.
Output file formats
SCF, FASTA, FASTQ, GenBank, EMBL, NEXUS, PHYLIP, and protein translations.
Trimming
Yes. Automated Phred/KB quality end clipping and vector trimming.
Integrated Blast
Yes. Submits selected reads or contigs directly to NCBI BLAST / MegaBLAST (up to ~8 kb via direct browser submission).
Open multiple windows
Yes, including Project View, Contig View, Trace View, Base View, Feature View, and Dot Plot windows.
Edit bases
Yes, with synchronized contig and trace editing.
ABI limits (regions outside of clear range region are displayed in gray)
Uses its own configurable End Clipping and quality thresholds rather than ABI clear-range grayed display.
Other functions
- Heterozygous SNP and indel detection (including trace subtraction)
- Trace sharpening, primer design, restriction mapping, and virtual cloning (Gibson/TOPO/HiFi)
- NGS reference alignment (Bowtie2) and bacterial scaffolding in newer v12–v13 releases
Cost
Paid perpetual licenses: $720 USD (Academic / Non-profit / Government) or $1,440 USD (Business), including Phred/Phrap licenses and 1 year of updates/support. A 30-day free trial and academic teaching/grant options are available.
Comments
CodonCode Aligner is one of the strongest dedicated commercial tools for Sanger contig assembly, heterozygous mutation/indel calling, and high-throughput trace editing. Unlike many older Windows/Mac tools, it remains actively maintained (v13.0) with native Apple Silicon macOS support.
Return to the Trace Viewers overview or check trace quality online with QualTrace III Online.