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Sequence type
DNA
Protein
Base substitution rates
JC
F81
K2P
HKY
TN
TNe
K3P
K3Pu
TPM2
TPM2u
TPM3
TPM3u
TIM
TIMe
TIM2
TIM2e
TIM3
TIM3e
TVM
TVMe
SYM
GTR
Base frequencies
-
F
FO
FQ
Rate heterogeneity across sites
-
I
G
I+G
R
I+R
Amino-acid exchange rate matrices
Blosum62
cpREV
Dayhoff
DCMut
FLU
HIVb
HIVw
JTT
JTTDCMut
LG
mtART
mtMAM
mtREV
mtZOA
mtMet
mtVer
mtInv
Poisson
PMB
rtREV
VT
WAG
GTR20
Protein mixture models
-
C10
C20
C30
C40
C50
C60
EX2
EX3
EHO
UL2
UL3
EX_EHO
LG4M
LG4X
CF4
Amino-acid frequencies
-
F
FO
FQ
Rate heterogeneity across sites
-
I
G
I+G
R
I+R
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logL
deltaL
bp-RELL
p-KH
p-SH
p-WKH
p-WSH
c-ELW
p-AU
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