Next: Refinements to substitution models
Up: Basepaired substitution models implemented
Previous: RNA7D model (Tillier, 98)
Contents
PHASE
contains a general 16state model (RNA16), however this model has free parameters
and is not well suited for phylogenetic inference, especially maximumlikelihood inference.
RNA16A is a simplified 16state model, it reduces some of the complexity of the RNA16
model by cutting down on the number of rate parameters from 120 to 5. It uses a rate
of single transitions , a rate of double transversions , a
mismatch
nonmismatch transition rate for transitions
requiring only one substitution and a mismatch
mismatch transition
rate for transitions requiring one substitution too. The reference rate is the rate of double transitions.
Some basepair substitutions are not allowed (null substitution rate).
The transition matrix for the RNA16A model is given in
table 2.10.
Table 2.10:
RNA16A transition matrix

GowriShankar Vivek
20030424