Performance of Aligners on the ROSETTA Dataset of 1160 Total Exons in Human and Mouse
| Aligner | 100% exons | 90% exons | 70% exons | Time (sec) |
| DIALIGN | 89 | 96 | 98 | 388 |
| MUMmer | 0 | 1 | 3 | 17 |
| GLASS | 91 | 97 | 98 | 154 |
| AVID | 90 | 95 | 97 | 19 |
| BlastZ | 94 | 97 | 98 | 17 |
| LAGAN | 94 | 97 | 98 | 48 |
[i] Columns show the percentage of exons annotated in human that are aligned to the orthologous mouse exon over at least 70%, 90%, and 100% of their length, and the time required to align the 129 sequences.