Table 3.
Standard genetic measures for Datasets 7–9
| Program | Clustal Ω | MARS+ Clustal Ω | MUSCLE | MARS+ MUSCLE |
|---|---|---|---|---|
| Dataset 7 | 50.2500.5 | 50.2500.5.rot | 50.2500.5 | 50.2500.5.rot |
| Length | 2,524 | 2,524 | 2,524 | 2,524 |
| PM Sites | 1,875 | 1,882 | 1,861 | 1,861 |
| Transitions | 86,781 | 87,190 | 86,628 | 86,628 |
| Transversions | 91,334 | 91,584 | 91,040 | 91,040 |
| Substitutions | 262,804 | 263,687 | 261,248 | 261,248 |
| Indels | 11,531 | 10,771 | 8,231 | 8,231 |
| AVPD | 223 | 224 | 219 | 219 |
| Dataset 8 | 50.2500.20 | 50.2500.20.rot | 50.2500.20 | 50.2500.20.rot |
| Length | 2,576 | 2,580 | 2,582 | 2,582 |
| PM Sites | 2,568 | 2,573 | 2,575 | 2,575 |
| Transitions | 284,302 | 284,667 | 282,638 | 282,670 |
| Transversions | 283,651 | 284,673 | 279,451 | 279,462 |
| Substitutions | 852,738 | 855,055 | 842,564 | 842,672 |
| Indels | 39,273 | 45,769 | 33,371 | 33,369 |
| AVPD | 728 | 735 | 715 | 715 |
| Dataset 9 | 50.2500.35 | 50.2500.35.rot | 50.2500.35 | 50.2500.35.rot |
| Length | 2,675 | 2,697 | 2,679 | 2,667 |
| PM Sites | 2,675 | 2,696 | 2,678 | 2,666 |
| Transitions | 424,910 | 423,592 | 426,230 | 426,063 |
| Transversions | 431,453 | 428,874 | 423,113 | 422,916 |
| Substitutions | 1,282,515 | 1,278,286 | 1,267,683 | 1,267,699 |
| Indels | 92,060 | 97,398 | 73,890 | 72,718 |
| AVPD | 1,122 | 1,123 | 1,095 | 1,094 |