in the name shows the number of parameters of the model): Model Rev? Freq Note 1.1 Yes 0 equiv. The following table shows the list of all Lie Markov models (the number before. Lie Markov models have a consistent property, which is lacking in other common models such as GTR. Starting with version 1.6, IQ-TREE supports a series of Lie Markov models ( Woodhams et al., 2015), many of which are non-reversible models. If users want to fix model parameters, append the model name with a curly bracket to fix the corresponding frequencies of A, C, G and T (must sum up to 1.0). The last rate, which corresponds to G-T, (and all rates with the same digit) is always set equal to 1.0 for convenience because the rates are relative. That means ‘101101’ describes the same matrix as ‘010010’. NOTE: The digits in the codes do not necessarily have to have the same order as above. Moreover, IQ-TREE supports arbitrarily restricted DNA model via a 6-digit code, e.g. 012345 is equivalent to GTR or SYM model as there is no restriction defined by such 6-digit code. Thus, 010010 is equivalent to K80 or HKY model (depending on whether base frequencies are equal or not). 010010 means that A-G rate is equal to C-T rate (corresponding to 1 in the code) and the remaining four substitution rates are equal (corresponding to 0 in the code). The last column Code is a 6-digit code defining the equality constraints for 6 relative substitution rates: A-C, A-G, A-T, C-G, C-T and G-T. 012345 GTR 8 General time reversible model with unequal rates and unequal base freq. 012314 SYM 5 Symmetric model with unequal rates but equal base freq. 012314 TVMe 4 Like TVM but equal base freq. 012032 TVM 7 Transversion model, AG=CT and unequal base freq. 012032 TIM3e 3 Like TIM3 but equal base freq. 010232 TIM3 6 AC=CG, AT=GT and unequal base freq. 010232 TIM2e 3 Like TIM2 but equal base freq. 012230 TIM2 6 AC=AT, CG=GT and unequal base freq. 012230 TIMe 3 Like TIM but equal base freq. 012012 TIM 6 Transition model, AC=GT, AT=CG and unequal base freq. 012012 TPM3u 5 Like TPM3 but unequal base freq. 010212 TPM3 2 AC=CG, AG=CT, AT=GT and equal base freq. 010212 TPM2u 5 Like TPM2 but unequal base freq. 012210 TPM2 2 AC=AT, AG=CT, CG=GT and equal base freq. 012210 K81u 5 Like K81 but unequal base freq. 010020 K81 or K3P 2 Three substitution types model and equal base freq. 010020 TNe 2 Like TN but equal base freq. 010010 TN or TN93 5 Like HKY but unequal purine/pyrimidine rates ( Tamura and Nei, 1993). 010010 HKY or HKY85 4 Unequal transition/transversion rates and unequal base freq. 000000 K80 or K2P 1 Unequal transition/transversion rates and equal base freq. 000000 F81 3 Equal rates but unequal base freq. IQ-TREE includes all common DNA models (ordered by complexity): Model df Explanation Code JC or JC69 0 Equal substitution rates and equal base frequencies ( Jukes and Cantor, 1969).
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