Table 3. Missing branch rates (%) and alignment SP-FN errors of ML methods on alignments the three largest biological datasets.
| Missing branch rate (%) | |||||
| Alignment | ML Method | 16S.B.ALL | 16S.T | 16S.3 | Average |
| TrueAln | RAxML | 0.0 | 0.0 | 0.0 | 0.0 |
| FastTree | 3.9 | 2.8 | 3.2 | 3.3 | |
| RAxML-Limited | 13.8 | 5.5 | 6.1 | 8.4 | |
| SATé | RAxML | n.d. | 7.5 | 6.8 | n.a. |
| FastTree | n.d. | 8.2 | 7.7 | n.a. | |
| RAxML-Limited | n.d. | 11.0 | 8.4 | n.a. | |
| MAFFT | RAxML | n.d. | 7.3 | n.d. | n.a. |
| FastTree | n.d. | 8.2 | n.d. | n.a. | |
| RAxML-Limited | n.d. | 8.9 | n.d. | n.a. | |
| PartTree | RAxML | 31.8 | 17.1 | 12.0 | 20.3 |
| FastTree | 29.1 | 16.3 | 12.5 | 19.3 | |
| RAxML-Limited | 38.4 | 18.6 | 15.4 | 24.1 | |
| ClustalW | RAxML | n.d. | 9.7 | 9.9 | n.a. |
| FastTree | n.d. | 10.5 | 10.4 | n.a. | |
| RAxML-Limited | n.d. | 12.9 | 13.3 | n.a. | |
| Quicktree | RAxML | 13.2 | 33.9 | 31.8 | 26.3 |
| FastTree | 13.5 | 33.9 | 32.5 | 26.6 | |
| RAxML-Limited | 21.8 | 35.0 | 35.6 | 30.8 | |
Only three alignment methods succeeded on the three largest biological datasets. For the other alignments that could not be successfully computed due to excessive memory requirements, topological accuracy of the ML methods were not available and thus not reported. “Average” refers to the average across the datasets. Entries for which no data was available because the alignment method failed to complete are marked “n.d.”. Averages that were not computed due to missing alignments for some datasets are marked “n.a.”. 
for each reported value other than the average.