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RNA6A model

Six state models completely ignore mismatches and consider substitutions between the six stable base-pairs only. Mismatch pairs are assigned to one of the 6 states in some deterministic fashion (the treatment of a mismatch is quite similar to the treatment of a gap with the DNA models). The RNA6A model is the most general six state model with 15 rate parameters and 6 frequencies (and 2 constraints) as shown in table 2.6.

Table 2.6: RNA6A transition matrix
Q = m_r \times \left(
...3} & \pi_{UG}\alpha_{14} & * \\

Gowri-Shankar Vivek 2003-04-24