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CBI of D. melanogaster were calculated using the preferred and unpreferred codon table implemented in the program.
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The within field index was calculated using the formula: Within-field index = (preferred−mean (non-preferred))/preferred.
The Bayes factor calculated using the path sampling method (log BF = −8.4) suggests the UCLN model (log marginal likelihood = −4384.83) is strongly preferred to the local clock model (log marginal likelihood = −4388.25).
Preferred codons for each genome and codon adaptation index (CAI) (Sharp and Li 1987) for all genes were calculated using the EMBOSS package (Rice et al. 2000).
Coverages were also calculated using the Genome Analysis Toolkit.
MBL was calculated using the equation (1).
I never calculated using the park as a setting, though.
The relative expression levels were calculated using the 2−ΔΔCt method2−ΔΔCt
The relative gene expression was calculated using the 2−ΔΔCt method83.
Statistical significance was calculated using the impaired t-test.
Average methylation level was calculated using the methylKit software package.
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