Modeling
2
In general, substitutions are more frequent between bases that are
biochemically more similar.
In the case of DNA, the four types of transition (A → G, G → A, C → T, T → C) are
usually more frequent than the eight
types of transversion (A → C, A → T, C → G, G → T, and the reverse). Such biases will affect the estimated divergence between
two sequences.
A
C
A
C
T
A
C
C
G
A
C
A
C
A
C
T
A
C
T
T
A
C
A
C
T
A
C
A
A
A
T
T
C
single
substitution
convergent
substitution
convergent
substitution
multiple
substitution
coincidental
substitution
parallel
substitution
conservation
ATGCTGTTAGGG
ATGCTCGTAGGG
MetLeuLeuGly
* *
ATGCT-GTTAGGGXX
ATGCTCGT-AGGGXX
MetLeuValArgXxx