Fig. 2
From: CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
The schematic overview of CNETS. AÂ Two modes of simulation implemented in CNETS. One is simulating CNPs directly for site duplication/deletion based on segments of variable size, which follows exactly the Markov model used for phylogeny inference. The other is simulating waiting times for events of multiple scales based on bins of fixed size, in which at most five types of events (site duplication/deletion, chromosome gain/loss, and WGD) are allowed and the duplication/deletion size in the number of bins is sampled from an exponential distribution of the user-specified mean size. BÂ The simulated tree and CNPs (red: duplication, blue: deletion, brown: normal), where coloured tips represent patient samples taken at different time points \(T_0\), \(T_1 = T_0 + n_1 * dt\), and \(T_2 = T_1 + n_2 * dt\), with dt, \(n_1\), and \(n_2\) being integers and \(1<= n_1, n_2 <= 6\,\text {(the number of samples)}\)