These notebooks collect code for the analyses performed in Zwaenepoel et al. (2019). Furthermore, our response to the original reply of Wang et al. to our manuscript is included (reply_wang_original.pdf). Note that the final (published) reply of Wang et al. (https://doi.org/10.1016/j.molp.2018.12.020) does not include the same figures as the original one, to which is referred in this response. However our arguments concerning isoform filtering and why our original concerns were not addressed in this original response are equally relevant to the published response by Wang et al.

Contents:

• dlsim.ipynb: code for a stochastic simulation of the birth-death model of duplicate gene demography of Lynch & Conery (2000).
• ks_modeling.ipynb: code for plotting and computing histograms, KDEs and Gaussian mixture models (GMMs) for K_S distributions
• reply_wang_original.pdf: our (unmodified) reply to the original response by Wang et al.