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Contents
Six state models completely ignore mismatches and consider
substitutions between the six stable basepairs 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

GowriShankar Vivek
20030424