Clustal Omega requires that each sequence in an alignment contain at least one residue that is not an ambiguity code.
- DNA sequences must contain at least one A, C, T or G.
- RNA sequences must contain at least one A, C, U, or G.
- Protein sequences must contain at least one A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W or Y.
If there are any sequences that do not meet this requirement, Clustal Omega will terminate with a “fatal error” message (visible in the MegAlign Pro Console), and no alignment will be created.
To address this issue, you can do either of the following:
- Remove the sequence and try aligning again with Clustal Omega.
- Include the sequence, but switch to MAFFT or MUSCLE as the alignment method. Neither of these algorithms requires sequences to contain at least one non-ambiguous residue.
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