Background Codon usage may vary significantly between different organisms and between
genes within the same organism. Several evolutionary processes have been postulated to …

We propose a simple, sensitive measure of synonymous codon usage bias, the Relative
Codon Adaptation Index (rCAI), as a way to discriminate better between highly biased and …

The vast amount of data generated by genome projects and the recent development of
population genetics models make comparative sequence analyses a very powerful …

The rate of molecular evolution can vary among lineages. Sources of this variation have
differential effects on synonymous and nonsynonymous substitution rates. Changes in …

Natural selection on codon usage is a pervasive force that acts on a large variety of
prokaryotic and eukaryotic genomes. Despite this, obtaining reliable estimates of selection …

Genomics profoundly affects most areas of biology, including ecology and evolutionary
biology. By examining genome sequences from multiple species, comparative genomics …

Background The nearly neutral theory of molecular evolution predicts that the efficacy of
natural selection increases with the effective population size. This prediction has been …

Both the overall rate of nucleotide substitution and the relative proportions of synonymous
and non-synonymous substitutions are predicted to vary between species that differ in …

Synonymous codon usage biases are associated with various biological factors, such as
gene expression level, gene length, gene translation initiation signal, protein amino acid …

It has been suggested that, due to the structure of the genetic code, nonsynonymous
transitions are less likely than transversions to cause radical changes in amino acid …