Execution time for different tree reconstruction methods on the LG+GC test set with alignments of length 500. For IQTree ModelFinder (MF) times were measured on the Cherry testing set (see section Performance Under More Realistic Models). For all methods except PF, total wall time was measured. For PF, the elapsed time is the sum of the time it takes to infer the distances and the time FastME takes to infer the tree from these distances. It is important to note that the distance prediction time does not include the time it takes to load the PF weights to the GPU as we did that once before inferring distances for all the testing alignments. The faded red dashed line shows the PF execution times, added to the average central processing unit (CPU) to GPU model-loading time measured over 100 replicates. The slight discrepancy noticeable at 110 leaves is due to a change of CPUs in our high performance computing (HPC) environment (see end of Baselines).