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
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