Divergence index (practical deviation/mean) away from Ka and you will Ks calculated based on the eight various methods about 12 vertebrate varieties

Divergence index (practical deviation/mean) away from Ka and you will Ks calculated based on the eight various methods about 12 vertebrate varieties

On the boxplots, straight down quantile, median, and you may top quantile have been depicted on the packets. Indicate thinking was basically illustrated from inside the dots. Outliers had been eliminated to make the area quick. The amount rules towards the vertebrate variety was: 1, chimp; 2, orangutan; 3, macaque; 4, horse; 5, dog; 6, cow; 7, guinea-pig; 8, mouse; nine, rat; 10, opossum; 11, platypus; and you will twelve, poultry.

The fresh new portion of common family genes off Ka, Ks and you can Ka/Ks according to GY weighed against most other 7 strategies in terms off clipped-regarding (A great, B), means (C, D), and you may species (Age, F). Outliers was removed to help make the plots easy. The number rules for the kinds are exactly the same as the what inside Figure step one.

This influence ideal that the Ka thinking haven’t contacted saturation yet

The methods used in this study cover a wide range of mutation models with different complexities. NG gives equal weight to every sequence variation path and LWL divides the mutation sites into three categories-non-degenerate, two-fold, and four-fold sites-and assigns fixed weights to synonymous and nonsynonymous sites for the two-fold degenerate sites . LPB adopts a flexible ratio of transitional to transversional substitutions to handle the two-fold sites [26, 27]. (más…)