Table 5.
Standard genetic measures for real data
| Program | Clustal Ω | MARS+ Clustal Ω | MUSCLE | MARS+ MUSCLE |
|---|---|---|---|---|
| Mammals | ||||
| Length | 19,452 | 18,829 | 19,784 | 19,180 |
| PM Sites | 12,913 | 12,265 | 13,076 | 12,454 |
| Transitions | 135,380 | 137,589 | 135,794 | 137,835 |
| Transversions | 81,945 | 84,188 | 76,894 | 78,067 |
| Substitutions | 295,684 | 302,331 | 282,608 | 286,747 |
| Indels | 82,494 | 59,348 | 91,164 | 71,042 |
| AVPD | 5729 | 5479 | 5663 | 5421 |
| Primates | ||||
| Length | 18,176 | 17,568 | 18,189 | 17,669 |
| PM Sites | 11,086 | 10,450 | 11,023 | 10,454 |
| Transitions | 259,921 | 261,995 | 262,179 | 264,245 |
| Transversions | 100,708 | 102,336 | 95,403 | 96,010 |
| Substitutions | 439,929 | 445,252 | 429,532 | 432,993 |
| Indels | 80,851 | 52,727 | 82,117 | 55,525 |
| AVPD | 4339 | 4149 | 4263 | 4070 |
| Viroids | ||||
| Length | 566 | 498 | 486 | 476 |
| PM Sites | 555 | 484 | 475 | 459 |
| Transitions | 7567 | 7485 | 9338 | 9101 |
| Transversions | 5837 | 5998 | 5491 | 5393 |
| Substitutions | 19,436 | 19,291 | 20,828 | 20,374 |
| Indels | 19,003 | 18,383 | 14,323 | 13,491 |
| AVPD | 251 | 246 | 229 | 221 |