Scripts to simulate neutral evolution with fixed genome sizes (Haegeman & Weitz, BMC Genomics, 2012)
The code can be used to simulate the gene frequency distribution arising from alternative models of genome evolution with fixed genome sizes. The code can also be used to infer the best fit parameters for alternative models given observed gene frequency data. The code is written in MATLAB. Note that the differential equation solver used in this version is ode45 which has greater numerical robustness, particularly for large datasets, when compared to ode15s (which is faster but may, in some instances, lead to numerical instabilities). The single .txt file attached should be separated into individual
Bart Haegeman and Joshua S Weitz (2012) A neutral theory of genome evolution and the frequency distribution of genes BMC Genomics 13:196.