Figure 5

Tree building algorithm comparison: NE vs E. Comparison of the Non-Exhaustive (NE), and Exhaustive (E) TAP approximation algorithms in tree building (Figure a), and TBR (Figure b). The patterns showed were observed in most of the combinations of simulation, algorithm, and edit distance parameters. a. Tree building using the Wagner algorithm. In every case, E outperformed NE, but the difference is not significant. However, as the branch lengths increased, the performance of the NE algorithm showed high variability (right), making E highly competitive for all distance functions with average branch length 0.3. b. Refinement using Union-pruning with NE and E. In this case, for almost every combination of algorithm, simulation, and distance function, E produce significantly shorter trees.