Figure 2.

The states of the "Plan 7" profile HMM. There are 3n + 4 states for a profile HMM representing a sequence family with n ancestral positions. Each internal position has three associated states: Match, Insertion, and Deletion. Additional states represent flanking insertions. All match and insertion states have an associated emission distribution, which is multinomial over the allowed residues. The insertion emission distributions typically reflect the background residue frequencies, while the match distributions are position-specific.

Edlefsen and Liu BMC Genomics 2010 11(Suppl 1):S10   doi:10.1186/1471-2164-11-S1-S10