Align sequences against reference MSA

Question

[kristjan]

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).

[Sej Modha]

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

[Joe]

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