Dear @stschiff
The factor 2 will cause the inconsistencies when plotting effective population size. And this has been disscussed here stschiff/msmc2#17 (comment). You should also update the Ne plot in the latest tutorial. Thank you very much.
lines(afrDat$left_time_boundary/mu*gen, (1/afrDat$lambda)/(2*mu), type="s", col="red")
Sincerely,
Zheng zhuqing