The probability of emitting each column in the alignment is defined by a sequence model returned by SelectModel(X, e, k, z, q, ψ). The current position k in alignment X, the end position of the scored interval (e), current state q, protein coding phase z, and phylogenetic parameters ψ determine the choice of sequence models. If q is an exon state and k is within the coding region, the coding phase z is 0, 1 or 2 and -1 otherwise. When q is an exon state and k is outside the coding region, an untranslated exon region is implied. The sequence models are divided into three "template" categories, MSige MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGnbqtdaWgaaWcbaGaem4uamLaemyAaKMaem4zaC2aaSbaaWqaaiabdwgaLbqabaaaleqaaaaa@3367@, Mcodon, and Mnon-coding and an instance of one of these three types is returned by the function: