Table 5. Missing branch rates (%) and alignment SP-FN errors ML methods on alignments of the six smallest biological datasets.
| Missing branch rate (%) | ||||||||
| Alignment | ML Method | 16S.M.aa_ag | 16S.M | 23S.M | 23S.M.aa_ag | 23S.E.aa_ag | 23S.E | Average |
| TrueAln | RAxML | 0.7 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.1 |
| FastTree | 1.6 | 0.7 | 5.4 | 3.2 | 3.3 | 9.3 | 3.9 | |
| RAxML-Limited | 3.7 | 3.8 | 11.9 | 5.1 | 12.1 | 10.7 | 7.9 | |
| SATé | RAxML | 4.8 | 6.9 | 10.7 | 11.5 | 9.9 | 4.0 | 8.0 |
| FastTree | 6.7 | 6.2 | 10.7 | 12.8 | 9.9 | 10.7 | 9.5 | |
| RAxML-Limited | 9.0 | 9.3 | 14.3 | 15.4 | 12.1 | 13.3 | 12.2 | |
| MAFFT | RAxML | 4.4 | 5.5 | 11.3 | 10.3 | 8.8 | 8.0 | 8.0 |
| FastTree | 7.4 | 5.7 | 10.7 | 9.6 | 13.2 | 12.0 | 9.8 | |
| RAxML-Limited | 8.8 | 6.2 | 16.7 | 13.5 | 13.2 | 20.0 | 13.0 | |
| PartTree | RAxML | 12.7 | 8.8 | 22.0 | 19.9 | 14.3 | 6.7 | 14.1 |
| FastTree | 12.9 | 8.6 | 22.6 | 18.6 | 17.6 | 12.0 | 15.4 | |
| RAxML-Limited | 12.9 | 10.0 | 22.6 | 19.9 | 19.8 | 17.3 | 17.1 | |
| ClustalW | RAxML | 13.9 | 11.2 | 16.7 | 16.0 | 22.0 | 17.3 | 16.2 |
| FastTree | 12.7 | 8.6 | 16.7 | 14.7 | 23.1 | 20.0 | 16.0 | |
| RAxML-Limited | 11.3 | 11.4 | 16.7 | 15.4 | 23.1 | 22.7 | 16.8 | |
| Quicktree | RAxML | 10.4 | 10.2 | 20.8 | 19.9 | 28.6 | 24.0 | 19.0 |
| FastTree | 11.5 | 9.3 | 19.6 | 17.9 | 18.7 | 20.0 | 16.2 | |
| RAxML-Limited | 10.6 | 10.0 | 20.2 | 17.9 | 25.3 | 20.0 | 17.3 | |
“Average” refers to the average across the six datasets. 
for each reported value other than the average.