Align sequences against reference MSA

What program can align a group of unaligned sequences against a large multiple sequence alignment? I need my sequences to have the same alignment length as the reference alignment, but they cannot be combined (like MAFFT -add does).

alignment msa

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updated 7.6 years ago by Biostar

• written 7.7 years ago by kristjan

Do you mean align one or more sequences to a consensus sequence generated using MSA?

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written 7.7 years ago by Sej Modha

I believe CLUSTAL's profile alignment mode can do this (you align new sequences against the existing alignment)

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written 7.7 years ago by Joe

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