… at a particular site is influenced by flanking codons, composition of 3ʹ flanking
nucleotide and amino acid content. In highly expressed plastid genes with a high overall …

… phylogenetic studies of codon usage bias where comparisons … nucleotide compositions
or for studies of codon usage bias in genomic regions that may differ in background nucleotide …

… in the evolution of biases in base composition and codon usage among large and small
viruses. Herein we conducted an analysis of the codon usage and nucleotide biases among all …

… nucleotide content of flanking regions and introns and mutational bias appears to be dominating
the evolution of codon usage… Often, the underlying nucleotide bias is not the focus of the …

… composition patterns could improve analysis of codon usage bias. A general rationale for
analyzing impact of (di)nucleotide bias on ENC is randomizing or shuffling synonymous …

… Given that ATP concentration is higher than that of the other three nucleotides in mitochondria,
we should expect synonymous codon usage to be biased toward A-ending codons …

… Correlation analysis is used to identify the relationship between codon usage bias and
synonymous codon usage pattern. This analysis is implemented based on the Spearman's rank …

… On the other hand, the differences in the nucleotide-ending ‘‘preferred’’ codon among amino
acids would have no effect on our results, as the only significant parameter in all measures, …

… to support them, and many apparent counterexamples), but any response to selection
would have to be at the level of mutational biases rather than individual nucleotides in genes. …

… a minor influence on codon usage bias. Comeron & Kreitman (… of codon usage bias, with
low bias in the middle but high bias … nucleotide-nucleotide interaction strength between codon …