Amino acid substitution models represent substitution rates among amino acids during the evolution. The models play an important role in analyzing protein sequences, especially inferring phylogenies. The rapid evolution of flaviviruses is expanding the threat in public health. A number of models have been estimated for some viruses, however, they are unable to properly represent amino acid substitution patterns of flaviviruses. In this study, we collected protein sequences from the flavivirus genus to specifically estimate an amino acid substitution model, called FLAVI, for flaviviruses. Experiments showed that the collected dataset was sufficient to estimate a stable model. More importantly, the FLAVI model was remarkably better than other existing models in analyzing flavivirus protein sequences. We recommend researchers to use the FLAVI model when studying protein sequences of flaviviruses or closely related viruses.

氨基酸替代模型表示进化过程中氨基酸之间的替代率。这些模型在分析蛋白质序列，尤其是推断系统发育方面发挥着重要作用。黄病毒的快速进化正在扩大对公共卫生的威胁。已经为某些病毒估计了许多模型，但是，它们无法正确表示黄病毒的氨基酸替代模式。在这项研究中，我们收集了来自黄病毒属的蛋白质序列，以专门估计黄病毒的氨基酸替代模型，称为 FLAVI。实验表明，收集到的数据集足以估计一个稳定的模型。更重要的是，FLAVI 模型在分析黄病毒蛋白质序列方面明显优于其他现有模型。