Description Usage Arguments Value
K80
This function creates the rate matrix of the K80 model before calculating the
related transition matrix, P, using the mutation (mu), branch length/time (t) and transition
transversion ratio (kappah)
1 |
t |
Branch length, i.e. specific generation time |
mu |
Mutation rate |
kappa |
ransition/transversion rate ratio |
pi |
Base Frequencies |
length |
Length of sequence that was used in creating the base frequencies. If provided the output will instead be the probability of mutation occuring |
This function returns a dgeMatrix
containing the transition matrix P, except if length is provided
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