An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias.

ABSTRACT: Phylogenetic codon models are routinely used to characterize selective regimes in coding sequences. Their parametric design, however, is still a matter of debate, in particular concerning the question of how to account for differing nucleotide frequencies and substitution rates. This problem relates to the fact that nucleotide composition in protein-coding sequences is the result of the interactions between mutation and selection. In particular, because of the structure of the genetic code, the nucleotide composition differs between the three coding positions, with the third position showing a more extreme composition. Yet, phylogenetic codon models do not correctly capture this phenomenon and instead predict that the nucleotide composition should be the same for all three positions. Alter

SUBMITTER: Latrille T 

PROVIDER: S-EPMC8831783 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature