Stupid question: nucleotide sequences

[MrTomRod]

Dear FAMSA2 developers

Thanks for your great tool! I'm happily using it for large protein sequence datasets.

It is never stated explicitly, but I suppose FAMSA2 is not made for nucleoteide sequences, right?

(Do you know of a similarly performant tool for nucleotide sequences?)

Best,
MrTomRod

[agudys]

Hello!

Glad to hear you are happy with our tool. Indeed, FAMSA is currently equipped only in amino acid substitution matrices. However, I know people use it successfully for nucleotide sequences (assuming they are subject to indels and substitutions only). Some time ago we did benchmarks on RNA sequences confirming FAMSA to be comparable to other algorithms equipped in nucleotide mode like Clustal or MAFFT. Thus, you can try FAMSA as it is on nucleotide sequences and check if it works for you.

That being said, adding a nucleotide model to FAMSA is one of our highest priorities so you can expect a proper nucleotide mode in FAMSA anytime soon.

Best,
Adam