4 votes

Which sequence alignment tools support codon alignment?

I don't know of any transcript-to-transcript aligners that are able to do this, but LAST can align transcript queries to protein reference sequences using a specified frameshift cost. Here's the ...
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2 votes

Which sequence alignment tools support codon alignment?

Try MACSE v2 (https://academic.oup.com/mbe/article/35/10/2582/5079334) will align multiple protein-coding nucleotide sequences based on their amino acid translation while allowing for the occurrence ...
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  • 121
2 votes

Which sequence alignment tools support codon alignment?

Virulign does this for virus sequences, the publication is available here and github address here
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