Here, we define a new amino aicd(AA) distance based on Ui, where Ui is from Tang et al. (2004).
The format of dUi.dat is same with miyata.dat in PAML. So we can use
the dUi as a new AA distance in PAML. See Exmaple for more
details.
The D_Ui has a high likelihood than the miyata’s and grantham’s
distance, thus D_Ui is a good AA distance than other distances from
AA’s physicochemical properties (See Chen et al. (2019),GBE).
See example codes for different AAs models in Example folder.
PAML 4.9 (by Ziheng Yang)
Please cite the follwing two papers.
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Chen Q, Lan A, Shen X, Wu C-I. 2019. Molecular evolution in small steps under prevailing negative selection - A nearly-universal rule of codon substitution. bioRxiv:https://doi.org/10.1101/510735.
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Chen Q, He Z, Lan A, Shen X, Wen H, Wu CI. 2019. Molecular evolution in large steps - Codon substitutions under positive selection. Mol Biol Evol:https://doi.org/10.1093/molbev/msz108.
- Tang H, Wyckoff GJ, Lu J, Wu CI. 2004. A universal evolutionary index for amino acid changes. Mol Biol Evol 21:1548-1556.