In the manuscript entitled “Do deleterious mutations promote the evolution of recombination suppression between X and Y chromosomes?” [1], the authors question the methodology and findings presented in our study on the role of deleterious mutations in the formation of sex chromosomes [2]. The present document is intended to answer the expressed concerns by explaining in more details why, in our Figure 3C [2], our approach was valid in setting aside: (1) simulations in which the inversion does not survive the first 20 generations; (2) simulations corresponding to the case « s=0 » (i.e., all mutations are neutral).