Figure 4

Comparison of approximation methods. Errors in P value approximation using different resampling replicates (indicated by the coloured lines), compared to that obtained by assuming a skew-normal distribution of MPD values (indicated as SN). Errors were strongly influenced by tip set size r, and weakly by tree size; on the left side appear the results for a 500 tip tree, and on the right for a 2000 tip tree). In most cases, P value approximation based on the skew-normal distribution performed better than the most commonly-used standard of 1000 set resamplings (blue line), and the relative performance of the skew-normal approach improved with increasing tip set size.