4

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 specific documentation for that option: -F COST Align DNA queries to protein reference sequences, using the specified frameshift cost. A value of 15 ...


2

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 of frameshifts


2

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


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