MODELING AMINO ACID SUBSTITUTIONS FOR WHOLE GENOMES

Authors

  • Le Sy Vinh VNU University of Engineering and Technology

DOI:

https://doi.org/10.15625/1813-9663/37/4/15937

Keywords:

Amino acid substitution model, whole genomes, maximum likelihood estimation methods, phylogenomics

Abstract

Modeling amino acid substitution process is a core task in bioinformatics. New advanced sequencing technologies have generated huge datasets including whole genomes from various species. Estimating amino acid substitution models from whole genome datasets provides us unprecedented opportunities to accurately investigate relationships among species. In this paper, we review state-of-the-art computational methods to estimate amino acid substitution models from large datasets. We also describe a comprehensive pipeline to practically estimate amino acid models from whole genome datasets. Finally, we apply amino acid substitution models to build phylogenomic trees from bird and plant genome datasets. We compare our newly reconstructed phylogenomic trees and published ones and discuss new findings.

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Published

2021-10-12

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Section

SPECIAL ISSUE DEDICATED TO THE MEMORY OF PROFESSOR PHAN DINH DIEU - PART B