SLAC
SLAC usage summary as of Fri Sep 3 00:00:00 2010
PST.
Top 10| Models used | Test results by p-value |
| HKY85 | 9026 | 51.5 | | 010000 | 2208 | 12.6 | | REV | 2045 | 11.7 | | F81 | 635 | 3.6 | | TRN93 | 525 | 3.0 | | 012212 | 288 | 1.6 | | 012012 | 206 | 1.2 | | 001101 | 186 | 1.1 | | 000010 | 134 | 0.8 | | 012032 | 121 | 0.7 |
|
| 0.1 | 1.0 | 12.5 | 13792 | 78.7 | | 0.05 | 0.9 | 7.4 | 2895 | 16.5 | | 0.25 | 1.2 | 35.7 | 212 | 1.2 | | 0.2 | 1.0 | 26.6 | 202 | 1.2 | | 0.01 | 0.7 | 9.2 | 112 | 0.6 | | 0.5 | 5.4 | 28.1 | 101 | 0.6 | | 0.3 | 1.2 | 24.0 | 94 | 0.5 | | 0.9 | 23.6 | 53.2 | 30 | 0.2 | | 0.15 | 2.5 | 32.4 | 17 | 0.1 | | 0.001 | 0.7 | 15.9 | 13 | 0.1 |
|
FEL
FEL usage summary as of Fri Sep 3 00:00:12 2010
PST.
Top 10| Models used | Test results by p-value |
| HKY85 | 8540 | 39.6 | | REV | 3305 | 15.3 | | 010000 | 2870 | 13.3 | | F81 | 918 | 4.3 | | TRN93 | 838 | 3.9 | | 012212 | 410 | 1.9 | | 012012 | 300 | 1.4 | | 000010 | 288 | 1.3 | | 001101 | 263 | 1.2 | | 010232 | 247 | 1.1 |
|
| 0.1 | 1.1 | 20.3 | 17760 | 82.4 | | 0.05 | 1.0 | 14.7 | 2856 | 13.3 | | 0.2 | 2.1 | 18.3 | 326 | 1.5 | | 0.25 | 3.1 | 35.3 | 246 | 1.1 | | 0.01 | 0.3 | 19.9 | 97 | 0.5 | | 0.5 | 5.1 | 38.8 | 77 | 0.4 | | 0.15 | 1.4 | 15.0 | 42 | 0.2 | | 0.19 | 0.2 | 4.5 | 14 | 0.1 | | 0.3 | 1.6 | 23.4 | 14 | 0.1 | | 0.06 | 0.8 | 10.1 | 14 | 0.1 |
|
REL
REL usage summary as of Fri Sep 3 00:00:27 2010
PST.
Top 10| Models used | Test results by Bayes Factor |
| HKY85 | 5652 | 44.3 | | 010000 | 1801 | 14.1 | | REV | 1431 | 11.2 | | F81 | 572 | 4.5 | | TRN93 | 523 | 4.1 | | 012012 | 242 | 1.9 | | 012212 | 217 | 1.7 | | 001101 | 185 | 1.4 | | 010232 | 125 | 1.0 | | 000010 | 120 | 0.9 |
|
| 50 | 4.0 | 22.8 | 10860 | 85.0 | | 10 | 6.5 | 33.7 | 434 | 3.4 | | 90 | 29.5 | 5.7 | 415 | 3.2 | | 20 | 9.8 | 34.0 | 368 | 2.9 | | 100 | 3.0 | 22.3 | 362 | 2.8 | | 95 | 3.1 | 21.5 | 97 | 0.8 | | 40 | 5.3 | 12.3 | 63 | 0.5 | | 0.1 | 54.0 | 82.6 | 48 | 0.4 | | 30 | 2.7 | 23.9 | 35 | 0.3 | | 25 | 8.7 | 17.2 | 18 | 0.1 |
|
TOGGLE
Toggle usage summary as of Fri Sep 3 00:00:35 2010
PST.
Model Selection
ModelSelection usage summary as of Fri Sep 3 00:00:36 2010
PST.
Top 10 Models
| HKY85 | 4270 | 30.2 |
| F81 | 1377 | 9.7 |
| TRN93 | 833 | 5.9 |
| 012212 | 604 | 4.3 |
| 010232 | 424 | 3.0 |
| 012232 | 394 | 2.8 |
| 012012 | 389 | 2.8 |
| 001101 | 363 | 2.6 |
| 010230 | 342 | 2.4 |
| 000010 | 340 | 2.4 |
Protein Model Selection
ModelSelectionP usage summary as of Fri Sep 3 00:00:42 2010
PST.
Top 10 Models
| JTT (Jones,Taylor,Thornton) | 93 | 23.0 |
| WAG (Whelan and Goldman) | 66 | 16.3 |
| LG (Le and Gascuel) | 62 | 15.3 |
| HIV (between hosts) | 46 | 11.4 |
| BLOSUM62 | 44 | 10.9 |
| HIV (within host) | 40 | 9.9 |
| IAV (Influenza A virus) | 17 | 4.2 |
| Dayhoff | 14 | 3.5 |
| VT (Vingron and Muller) | 8 | 2.0 |
| rtREV (reverse transcriptase) | 6 | 1.5 |
GARD
GARD usage summary as of Fri Sep 3 00:00:43 2010
PST.
| Top 10 models used | Distribution of delta AIC | Number of inferred breakpoints |
| 0 | 6018 | 50.7 | | HKY85 | 2995 | 25.2 | | 010000 | 430 | 3.6 | | REV | 415 | 3.5 | | TRN93 | 279 | 2.4 | | F81 | 260 | 2.2 | | 010232 | 113 | 1.0 | | 012212 | 109 | 0.9 | | 010230 | 91 | 0.8 | | 012232 | 72 | 0.6 |
|
| 0-10 | 3683 | 31.0 | | 10-20 | 533 | 4.5 | | 20-30 | 436 | 3.7 | | 30-40 | 398 | 3.4 | | 40-50 | 328 | 2.8 | | 50-60 | 302 | 2.5 | | 60-70 | 237 | 2.0 | | 70-80 | 199 | 1.7 | | 80-90 | 208 | 1.8 | | 90-100 | 155 | 1.3 | | > 100 | 5383 | 45.4 |
|
| 0 | 2920 | 24.6 | | 1 | 2797 | 23.6 | | 2 | 2056 | 17.3 | | 3 | 1274 | 10.7 | | 4 | 822 | 6.9 | | 5 | 566 | 4.8 | | 6 | 379 | 3.2 | | 7 | 257 | 2.2 | | 8 | 155 | 1.3 | | 9 | 153 | 1.3 | | ≥ 10 | 483 | 4.1 |
|
SBP
SBP usage summary as of Fri Sep 3 00:00:51 2010
PST.
| Top 10 models used | Distribution of IC improvement |
| HKY85 | 2437 | 46.7 | | REV | 614 | 11.8 | | 010000 | 380 | 7.3 | | F81 | 266 | 5.1 | | TRN93 | 239 | 4.6 | | 010232 | 124 | 2.4 | | 012212 | 76 | 1.5 | | 012232 | 66 | 1.3 | | 010212 | 63 | 1.2 | | 010230 | 58 | 1.1 |
|
| 0-10 | 2095 | 40.2 | | 10-20 | 251 | 4.8 | | 20-30 | 209 | 4.0 | | 30-40 | 160 | 3.1 | | 40-50 | 149 | 2.9 | | 50-60 | 124 | 2.4 | | 60-70 | 86 | 1.6 | | 70-80 | 91 | 1.7 | | 80-90 | 63 | 1.2 | | 90-100 | 66 | 1.3 | | > 100 | 1921 | 36.8 |
|
PARRIS
PARRIS usage summary as of Fri Sep 3 00:00:55 2010
PST.
| Top 10 models used | Distribution of p-values |
| HKY85 | 1556 | 48.8 | | 010000 | 301 | 9.4 | | REV | 254 | 8.0 | | F81 | 188 | 5.9 | | TRN93 | 139 | 4.4 | | 012212 | 76 | 2.4 | | 012012 | 62 | 1.9 | | 012232 | 36 | 1.1 | | 012030 | 35 | 1.1 | | 001101 | 27 | 0.8 |
|
| 0-0.1 | 609 | 19.1 | | 0.1-0.2 | 123 | 3.9 | | 0.2-0.3 | 145 | 4.5 | | 0.3-0.4 | 79 | 2.5 | | 0.4-0.5 | 93 | 2.9 | | 0.5-0.6 | 76 | 2.4 | | 0.6-0.7 | 87 | 2.7 | | 0.7-0.8 | 95 | 3.0 | | 0.8-0.9 | 92 | 2.9 | | 0.9-1 | 1789 | 56.1 |
|
GA Branch
GABranch usage summary as of Fri Sep 3 00:00:57 2010
PST.
| Top 10 models used | Distribution of the number of dN/dS classes |
| HKY85 | 1462 | 42.5 | | REV | 471 | 13.7 | | 010000 | 371 | 10.8 | | F81 | 160 | 4.6 | | TRN93 | 144 | 4.2 | | 012012 | 66 | 1.9 | | 001101 | 48 | 1.4 | | 012232 | 42 | 1.2 | | 012032 | 38 | 1.1 | | 000010 | 35 | 1.0 |
|
| 1 | 4 | 0.1 | | 2 | 1235 | 35.9 | | 3 | 1225 | 35.6 | | 4 | 647 | 18.8 | | 5 | 217 | 6.3 | | 6 | 75 | 2.2 | | 7 | 28 | 0.8 | | 8 | 10 | 0.3 | | 9 | 0 | 0.0 |
|
CMS
CMS usage summary as of Fri Sep 3 00:00:59 2010
PST.
| Distribution of mBIC improvement | Number of inferred rate classes |
| 0-10 | 10 | 3.4 | | 10-20 | 12 | 4.1 | | 20-30 | 13 | 4.5 | | 30-40 | 22 | 7.5 | | 40-50 | 21 | 7.2 | | 50-60 | 21 | 7.2 | | 60-70 | 16 | 5.5 | | 70-80 | 13 | 4.5 | | 80-90 | 22 | 7.5 | | 90-100 | 14 | 4.8 | | > 100 | 128 | 43.8 |
|
| 1 | 0 | 0.0 | | 2 | 193 | 66.1 | | 3 | 62 | 21.2 | | 4 | 22 | 7.5 | | 5 | 8 | 2.7 | | 6 | 2 | 0.7 | | 7 | 2 | 0.7 | | 8 | 0 | 0.0 | | 9 | 0 | 0.0 | | ≥ 10 | 3 | 1.0 |
|
DEPS
DEPS usage summary as of Fri Sep 3 00:00:59 2010
PST.
Co-evolution
BGM usage summary as of Fri Sep 3 00:01:00 2010
PST.
Wayne Delport, Art Poon, Simon D.W. Frost and Sergei L. Kosakovsky Pond, 2004-2010