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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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