Figure 3.

New alignment confidence display. The colour of the residues reflects the alignment uncertainty, and is based on the posterior probability that is calculated by HMMER3. A green residue indicates a high posterior probability which means that the alignment of the amino acid to the match/insert state in the profile HMM is very likely to be correct. Where the posterior probablity is lower, and therefore the alignment certainty decreases, the colour becomes closer to red. This allows users quickly to identify regions of the alignment where some sequences are aligned with less certainty.