Perform optimal global alignment of two coding sequences using a codon substitution matrix and configurable gap penalties.
Paste the first coding sequence (FASTA or raw). Only A, C, G, T/U are retained (limit 6,000,000 characters).
Paste the second coding sequence (FASTA or raw). Only A, C, G, T/U are retained (limit 6,000,000 characters).
Penalty applied to gaps preceding a sequence.
Penalty applied to internal gaps.
Penalty applied to gaps following a sequence.
Paste two DNA sequences in FASTA or raw format. Sequences must be multiples of 3 bases (complete codons) and can be up to 6 million characters each.
Set gap penalties for leading, internal, and trailing positions. Leading and trailing gaps are often set to 0 for global alignment, while internal gaps penalize insertions/deletions.
Click execute to align sequences using the Schneider et al. (2005) codon substitution matrix. Alignment operates at the codon level rather than individual nucleotides.
Results display aligned codon triplets with gaps shown as ".--" and an overall alignment score reflecting codon similarity and gap costs.
This tool aligns coding sequences by codon, using the substitution matrix described by Schneider et al. (2005). Gap penalties are applied at the codon level and may be adjusted to explore different alignment sensitivities.
The output retains codon triplets, inserting the placeholder `.--` to denote codon-sized gaps. The reported alignment score reflects the chosen gap penalties and matrix entries.