Fig. 2: Impact of marker selection parameters on trees inferred from simulated data.
From: Augmenting microbial phylogenomic signal with tailored marker gene sets
a Contour plots of the mean normalized Robinson-Foulds (nRF) distance between inferred and real trees from simulated datasets of 50 gene families from 10 genomes across n = 25 replicates. b Contour plots of the mean nRF distance between inferred and real (top) and proportion of confident branches in inferred trees (bottom) from simulations of realistic prokaryotic gene families across n = 25 replicates. Marker selection was applied to each combination of the number of markers (k) and exponent (p). Each plot illustrates a scenario with different noise levels in gene trees (a, b) and maximum copies of gene families (only a). Source data are provided as a Source Data file.
