Pairwise Align Codons

First coding DNA sequence

Second coding DNA sequence

Genetic codeGap openingGap extension

Output

How to align two coding sequences by codon

Paste the two coding DNA sequences, in frame.
Choose the genetic code and the gap penalties.
Click Align. The proteins are aligned and the gaps copied back to the DNA, so codons stay whole.

Frequently asked questions

Why align codons instead of bases?

An alignment of bases can put gaps in the middle of codons. Aligning the proteins first keeps each codon together, which is what dN/dS and other codon-based analyses need.

Is my sequence uploaded?

No. Everything runs in your browser, so your sequences never leave your device.

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