aspartik.b3.substitutions
class HKY:
#Hasegawa et al. 1985
A model which can be thought of as a combination of K80 and F81: both base rates and transition/transversion ratio are configurable.
Hasegawa et al. 1985, Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, https://doi.org/10.1007/BF02101694.
frequencies
#DNA nucleotide frequencies
Must have the length of 4, with each element corresponding to Adenine, Cytosine, Guanine, and Thymine respectively.
class JC:
#Jukes-Cantor
A simple model with equal state transition rates.
Jukes and Cantor 1969, Evolution of Protein Molecules, https://doi.org/10.1016/b978-1-4832-3211-9.50009-7.
class K80:
#Kimura 80
Equal base frequencies (A/C/G/T) with different transition (keeps purines/pyrimidines) and transversion (purine to pyrimidine and visa versa).
Kimura 1980, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, https://doi.org/10.1007/BF01731581.