gravatar for Mensur Dlakic

4 hours ago by

USA

Opinions differ about this, but MAFFT - or any "regular" sequence alignment program - is generally not able to align 16S sequences properly unless they are from fairly related species. It is not a matter of codon alignment - something that understands sequence co-variation is needed to align 16S sequences properly.

SSU-ALIGN can search for 16S sequences and automatically align them based on their phylogenetic membership.



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