Fig. 1.

Illustration of the various tools and visualizations in wgd. (A) Arabidopsis thaliana and Carica papaya paranome K_S distributions overlayed with the K_S distribution of anchor pairs for A. thaliana and K_S distribution of one-to-one orthologs of C. papaya and A. thaliana. (B) Mixture of three log-normal distributions fitted to the K_S distribution of A. thaliana, using the Variational Bayes algorithm with γ = 10⁻³. (C) Plot showing the probability to belong to a particular component of the mixture shown in (B) in function of K_S. These probabilities can be used to define component-wise paralogs for further downstream analyses. (D) K_S-colored dotplot for A. thaliana, showing colinear blocks identified by I-ADHoRe, colored by their median K_S value. (E) Interactive histogram visualization (user interface not shown, see Supplementary Fig. S1), showing the whole paranome K_S distributions using histograms and kernel density estimates for A. thaliana and C. papaya together with the K_S distribution of one-to-one orthologs in these species. We refer to the Supplementary Material for detailed methods