Abstract
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.
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Data Availability
The FLAVI data is available at https://github.com/thulekm/flavi
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Acknowledgements
This research is funded by Vietnam National Foundation for Science and Technology Development (NAFOSTED) under Grant number 102.01.2019.06.
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VLS designed the study and experiments. LKT performed experiments. Both authors analyzed experimental results, wrote and approved the final manuscript.
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Handling Editor: Keith Crandall.
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Le, T.K., Vinh, L.S. FLAVI: An Amino Acid Substitution Model for Flaviviruses. J Mol Evol 88, 445–452 (2020). https://doi.org/10.1007/s00239-020-09943-3
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DOI: https://doi.org/10.1007/s00239-020-09943-3