Analysis of the codon usage of overlapping frames from the benchmark dataset.

Abbreviations are the same as in Table 1. The last two overlaps have entered their genome by horizontal transfer (see text).rsA is the Spearman rank correlation coefficient rs between the codon usage of the ancestral frame and that of its genome. rsN is the equivalent coefficient for the de novo frame. NA and NN are the number of codons on which rsA and rsN were calculated. The first row indicates whether calculations are presented for the actual overlapping frames or for the corresponding simulated frames. The calculation of P for the actual frames is based on Hotelling's t-test, whereas for simulated frames P is based on the distribution of the simulated d21 (see text). Agreement between t-Hotelling and simulation is calculated on the basis of whether corresponding P-values are both 0.05.