Selectional explaination
removal by natural selection
Saturation explaination
many mutations on same site
Models of evolution
allow to sample data to compensate for real life bias
2 main variables of models of evolution
probability of mutations (costs of substitutions)
frequency of bases
Jukes-Cantor (JC)
equal frequency of bases
all susbtitutions equal
Kimura 2 parameter (K2P)
equal frequency of bases
transitions not equal to transversions
Felsenstein 1981 (F81)
different for each base
all susbtitutions equal
Hasegawa, Kishino, Yano (HKY48)
different for each base
transitions not equal to transversions
General Reversible (GTR)
different for each base
different for each type of substitution
Additional parameters
I: rate proportion of invariable sites
G: gamma distributions: allows to show different mutation rates
Assumptions
1. independence: mutations in one part of DNA, compensation mutation, Mutation in one site -> impact another.
2. Base composition: GC bias
3. variation in rates of substitution among sites