SLAC
SLAC usage summary as of Fri Oct 10 00:00:01 2008
PST.
Top 10| Models used | Test results by p-value |
| HKY85 | 10470 | 53.1 | | 010000 | 2443 | 12.4 | | REV | 2377 | 12.0 | | TRN93 | 618 | 3.1 | | F81 | 578 | 2.9 | | 012212 | 318 | 1.6 | | 001101 | 176 | 0.9 | | 012012 | 167 | 0.8 | | 010232 | 146 | 0.7 | | 012232 | 125 | 0.6 |
|
| 0.1 | 0.9 | 12.8 | 16067 | 81.4 | | 0.05 | 0.9 | 8.5 | 2850 | 14.4 | | 0.25 | 1.4 | 32.8 | 240 | 1.2 | | 0.2 | 1.2 | 27.7 | 169 | 0.9 | | 0.5 | 5.2 | 26.4 | 110 | 0.6 | | 0.3 | 1.2 | 24.6 | 84 | 0.4 | | 0.01 | 0.5 | 8.0 | 53 | 0.3 | | 0.9 | 24.9 | 50.4 | 31 | 0.2 | | 0.15 | 2.1 | 23.4 | 26 | 0.1 | | 50 | 11.6 | 31.2 | 8 | 0.0 |
|
FEL
FEL usage summary as of Fri Oct 10 00:00:16 2008
PST.
Top 10| Models used | Test results by p-value |
| HKY85 | 4257 | 41.5 | | REV | 1522 | 14.8 | | 010000 | 1159 | 11.3 | | F81 | 422 | 4.1 | | TRN93 | 374 | 3.6 | | 012212 | 218 | 2.1 | | 000010 | 183 | 1.8 | | 001101 | 166 | 1.6 | | 012012 | 132 | 1.3 | | 010232 | 127 | 1.2 |
|
| 0.1 | 1.0 | 20.8 | 8608 | 83.9 | | 0.05 | 0.8 | 13.9 | 1200 | 11.7 | | 0.25 | 2.7 | 36.8 | 174 | 1.7 | | 0.2 | 1.6 | 27.0 | 107 | 1.0 | | 0.15 | 1.5 | 15.4 | 37 | 0.4 | | 0.5 | 5.3 | 31.7 | 33 | 0.3 | | 0.01 | 0.7 | 19.0 | 29 | 0.3 | | 0.19 | 0.2 | 4.5 | 14 | 0.1 | | 0.95 | 33.8 | 25.7 | 8 | 0.1 | | 0.005 | 0.3 | 10.5 | 7 | 0.1 |
|
REL
REL usage summary as of Fri Oct 10 00:00:23 2008
PST.
Top 10| Models used | Test results by Bayes Factor |
| HKY85 | 2714 | 46.4 | | 010000 | 933 | 16.0 | | REV | 417 | 7.1 | | TRN93 | 233 | 4.0 | | F81 | 219 | 3.7 | | 012212 | 96 | 1.6 | | 001101 | 90 | 1.5 | | 012012 | 87 | 1.5 | | 000010 | 78 | 1.3 | | 010232 | 58 | 1.0 |
|
| 50 | 3.2 | 20.5 | 4980 | 85.2 | | 10 | 6.1 | 35.0 | 314 | 5.4 | | 100 | 4.8 | 23.2 | 181 | 3.1 | | 20 | 16.1 | 17.1 | 155 | 2.7 | | 95 | 3.2 | 20.4 | 83 | 1.4 | | 0.1 | 65.8 | 93.0 | 35 | 0.6 | | 90 | 5.2 | 6.7 | 27 | 0.5 | | 40 | 1.5 | 20.1 | 18 | 0.3 | | 30 | 0.4 | 39.8 | 15 | 0.3 | | 5 | 9.2 | 27.9 | 7 | 0.1 |
|
Model Selection
ModelSelection usage summary as of Fri Oct 10 00:00:44 2008
PST.
Top 10 Models
| HKY85 | 1292 | 31.3 |
| F81 | 341 | 8.3 |
| TRN93 | 271 | 6.6 |
| 012212 | 205 | 5.0 |
| 000010 | 131 | 3.2 |
| 001101 | 118 | 2.9 |
| 010232 | 113 | 2.7 |
| 012232 | 101 | 2.4 |
| 012012 | 93 | 2.3 |
| 012032 | 75 | 1.8 |
Protein Model Selection
ModelSelectionP usage summary as of Fri Oct 10 00:00:46 2008
PST.
Top 10 Models
| WAG (Whelan and Goldman) | 20 | 24.1 |
| LG (Le and Gascuel) | 17 | 20.5 |
| HIV (between hosts) | 16 | 19.3 |
| JTT (Jones,Taylor,Thornton) | 16 | 19.3 |
| BLOSUM62 | 6 | 7.2 |
| HIV (within host) | 3 | 3.6 |
| mtMAM (mammalian mitochondrial) | 1 | 1.2 |
| IAV (Influenza A virus) | 1 | 1.2 |
| Dayhoff | 1 | 1.2 |
| rtREV (reverse transcriptase) | 1 | 1.2 |
PARRIS
PARRIS usage summary as of Fri Oct 10 00:00:47 2008
PST.
| Top 10 models used | Distribution of p-values |
| HKY85 | 511 | 50.5 | | 010000 | 83 | 8.2 | | TRN93 | 53 | 5.2 | | REV | 51 | 5.0 | | F81 | 45 | 4.4 | | 012212 | 40 | 4.0 | | 012012 | 23 | 2.3 | | 012232 | 13 | 1.3 | | 012032 | 12 | 1.2 | | 000010 | 12 | 1.2 |
|
| 0-0.1 | 218 | 21.5 | | 0.1-0.2 | 38 | 3.8 | | 0.2-0.3 | 31 | 3.1 | | 0.3-0.4 | 28 | 2.8 | | 0.4-0.5 | 35 | 3.5 | | 0.5-0.6 | 21 | 2.1 | | 0.6-0.7 | 21 | 2.1 | | 0.7-0.8 | 36 | 3.6 | | 0.8-0.9 | 27 | 2.7 | | 0.9-1 | 557 | 55.0 |
|
GA Branch
GABranch usage summary as of Fri Oct 10 00:00:48 2008
PST.
| Top 10 models used | Distribution of the number of dN/dS classes |
| HKY85 | 560 | 49.7 | | REV | 107 | 9.5 | | 010000 | 93 | 8.3 | | F81 | 49 | 4.3 | | TRN93 | 39 | 3.5 | | 012012 | 31 | 2.8 | | 000010 | 25 | 2.2 | | 012032 | 20 | 1.8 | | 011020 | 16 | 1.4 | | 012232 | 14 | 1.2 |
|
| 1 | 1 | 0.1 | | 2 | 392 | 34.8 | | 3 | 427 | 37.9 | | 4 | 202 | 17.9 | | 5 | 64 | 5.7 | | 6 | 29 | 2.6 | | 7 | 10 | 0.9 | | 8 | 2 | 0.2 | | 9 | 0 | 0.0 |
|
Co-evolution
BGM usage summary as of Fri Oct 10 00:00:49 2008
PST.
Sergei L. Kosakovsky Pond, Art Poon and Simon D.W. Frost, 2004-2008