Open AccessMODELING AMINO ACID SUBSTITUTIONS FOR WHOLE GENOMES
Author(s) -
Lê Sỹ Vinh
Publication year - 2021
Publication title -
journal of computer science and cybernetics (vietnam academy of science and technology)/journal of computer science and cybernetics
Language(s) - English
Resource type - Journals
eISSN - 2815-5939
pISSN - 1813-9663
DOI - 10.15625/1813-9663/37/4/15937
Subject(s) - genome , pipeline (software) , substitution (logic) , computational biology , computer science , amino acid , amino acid substitution , task (project management) , biology , data mining , genetics , gene , mutation , engineering , systems engineering , programming language
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.