SLAC
SLAC usage summary as of Mon Feb 6 00:00:01 2012
PST.
Top 10| Models used | Test results by p-value |
| HKY85 | 2066 | 60.9 | | REV | 409 | 12.1 | | TRN93 | 190 | 5.6 | | F81 | 116 | 3.4 | | 012012 | 64 | 1.9 | | 010232 | 43 | 1.3 | | 012212 | 37 | 1.1 | | 012010 | 32 | 0.9 | | 012032 | 30 | 0.9 | | 012030 | 29 | 0.9 |
|
| 0.1 | 0.5 | 13.3 | 2860 | 84.4 | | 0.05 | 1.0 | 11.5 | 357 | 10.5 | | 0.2 | 2.9 | 65.2 | 110 | 3.2 | | 0.25 | 0.4 | 2.9 | 43 | 1.3 | | 0.5 | 26.3 | 42.9 | 6 | 0.2 | | 0.01 | 0.0 | 5.2 | 5 | 0.1 | | 0.3 | 0.1 | 1.0 | 3 | 0.1 | | 0 | 0.0 | 0.0 | 2 | 0.1 | | 0.001 | 0.0 | 0.0 | 1 | 0.0 | | 0.9 | 16.7 | 50.0 | 1 | 0.0 |
|
FEL
FEL usage summary as of Mon Feb 6 00:00:05 2012
PST.
Top 10| Models used | Test results by p-value |
| HKY85 | 14116 | 42.0 | | REV | 5078 | 15.1 | | 010000 | 3726 | 11.1 | | TRN93 | 1643 | 4.9 | | F81 | 1340 | 4.0 | | 012212 | 593 | 1.8 | | 010232 | 519 | 1.5 | | 012012 | 496 | 1.5 | | 001101 | 388 | 1.2 | | 000010 | 366 | 1.1 |
|
| 0.1 | 1.1 | 20.8 | 27446 | 81.7 | | 0.05 | 1.1 | 16.9 | 4603 | 13.7 | | 0.2 | 2.5 | 36.0 | 603 | 1.8 | | 0.25 | 3.1 | 30.5 | 364 | 1.1 | | 0.01 | 0.3 | 19.0 | 186 | 0.6 | | 0.5 | 5.9 | 44.9 | 112 | 0.3 | | 0.15 | 1.1 | 21.9 | 58 | 0.2 | | 0.3 | 1.2 | 31.0 | 35 | 0.1 | | 0.06 | 0.8 | 10.1 | 14 | 0.0 | | 0.19 | 0.2 | 4.5 | 14 | 0.0 |
|
REL
REL usage summary as of Mon Feb 6 00:00:26 2012
PST.
Top 10| Models used | Test results by Bayes Factor |
| HKY85 | 10547 | 49.6 | | REV | 2287 | 10.7 | | 010000 | 2235 | 10.5 | | TRN93 | 974 | 4.6 | | F81 | 883 | 4.1 | | 012012 | 391 | 1.8 | | 012212 | 318 | 1.5 | | 001101 | 315 | 1.5 | | 010232 | 202 | 0.9 | | 000010 | 191 | 0.9 |
|
| 50 | 3.9 | 23.7 | 18862 | 88.6 | | 100 | 2.9 | 21.4 | 558 | 2.6 | | 10 | 6.2 | 31.9 | 511 | 2.4 | | 20 | 9.4 | 35.0 | 458 | 2.2 | | 90 | 28.6 | 6.9 | 428 | 2.0 | | 95 | 2.4 | 24.6 | 137 | 0.6 | | 40 | 4.9 | 14.9 | 69 | 0.3 | | 0.1 | 51.7 | 78.2 | 52 | 0.2 | | 30 | 14.5 | 21.9 | 46 | 0.2 | | 25 | 5.0 | 35.7 | 35 | 0.2 |
|
TOGGLE
Toggle usage summary as of Mon Feb 6 00:00:38 2012
PST.
Model Select.
ModelSelection usage summary as of Mon Feb 6 00:00:39 2012
PST.
Top 10 Models
| HKY85 | 7330 | 28.7 |
| F81 | 2226 | 8.7 |
| TRN93 | 1885 | 7.4 |
| 010232 | 983 | 3.8 |
| 012212 | 980 | 3.8 |
| 012012 | 770 | 3.0 |
| 001101 | 671 | 2.6 |
| 012232 | 662 | 2.6 |
| 000010 | 612 | 2.4 |
| 010230 | 567 | 2.2 |
Protein Model Select.
ModelSelectionP usage summary as of Mon Feb 6 00:00:50 2012
PST.
Top 10 Models
| JTT (Jones,Taylor,Thornton) | 135 | 14.9 |
| JTT (Jones,Taylor,Thornton)+F | 90 | 9.9 |
| WAG (Whelan and Goldman) | 86 | 9.5 |
| LG (Le and Gascuel) | 71 | 7.8 |
| WAG (Whelan and Goldman)+F | 66 | 7.3 |
| IAV (Influenza A virus) | 57 | 6.3 |
| HIV (between hosts) | 55 | 6.1 |
| BLOSUM62 | 54 | 5.9 |
| HIV (within host) | 48 | 5.3 |
| BLOSUM62+F | 41 | 4.5 |
GARD
GARD usage summary as of Mon Feb 6 00:00:52 2012
PST.
| Top 10 models used | Distribution of delta AIC | Number of inferred breakpoints |
| 0 | 12495 | 68.1 | | HKY85 | 2995 | 16.3 | | 010000 | 430 | 2.3 | | REV | 415 | 2.3 | | TRN93 | 279 | 1.5 | | F81 | 260 | 1.4 | | 010232 | 113 | 0.6 | | 012212 | 109 | 0.6 | | 010230 | 91 | 0.5 | | 012232 | 72 | 0.4 |
|
| 0-10 | 5984 | 32.6 | | 10-20 | 797 | 4.3 | | 20-30 | 677 | 3.7 | | 30-40 | 590 | 3.2 | | 40-50 | 475 | 2.6 | | 50-60 | 414 | 2.3 | | 60-70 | 354 | 1.9 | | 70-80 | 349 | 1.9 | | 80-90 | 317 | 1.7 | | 90-100 | 267 | 1.5 | | > 100 | 8115 | 44.2 |
|
| 0 | 4806 | 26.2 | | 1 | 4364 | 23.8 | | 2 | 3183 | 17.4 | | 3 | 1881 | 10.3 | | 4 | 1171 | 6.4 | | 5 | 813 | 4.4 | | 6 | 538 | 2.9 | | 7 | 376 | 2.1 | | 8 | 244 | 1.3 | | 9 | 214 | 1.2 | | ≥ 10 | 749 | 4.1 |
|
SBP
SBP usage summary as of Mon Feb 6 00:01:04 2012
PST.
| Top 10 models used | Distribution of IC improvement |
| HKY85 | 3530 | 43.7 | | REV | 1187 | 14.7 | | 010000 | 564 | 7.0 | | TRN93 | 421 | 5.2 | | F81 | 402 | 5.0 | | 010232 | 177 | 2.2 | | 012012 | 105 | 1.3 | | 012232 | 94 | 1.2 | | 012212 | 91 | 1.1 | | 010230 | 91 | 1.1 |
|
| 0-10 | 3405 | 42.2 | | 10-20 | 382 | 4.7 | | 20-30 | 302 | 3.7 | | 30-40 | 266 | 3.3 | | 40-50 | 208 | 2.6 | | 50-60 | 170 | 2.1 | | 60-70 | 146 | 1.8 | | 70-80 | 137 | 1.7 | | 80-90 | 107 | 1.3 | | 90-100 | 98 | 1.2 | | > 100 | 2853 | 35.3 |
|
PARRIS
PARRIS usage summary as of Mon Feb 6 00:01:09 2012
PST.
| Top 10 models used | Distribution of p-values |
| HKY85 | 2914 | 53.6 | | 010000 | 400 | 7.4 | | REV | 370 | 6.8 | | F81 | 287 | 5.3 | | TRN93 | 257 | 4.7 | | 012212 | 95 | 1.7 | | 012012 | 90 | 1.7 | | 001101 | 77 | 1.4 | | 012232 | 60 | 1.1 | | 010232 | 59 | 1.1 |
|
| 0-0.1 | 920 | 16.9 | | 0.1-0.2 | 190 | 3.5 | | 0.2-0.3 | 199 | 3.7 | | 0.3-0.4 | 143 | 2.6 | | 0.4-0.5 | 150 | 2.8 | | 0.5-0.6 | 157 | 2.9 | | 0.6-0.7 | 151 | 2.8 | | 0.7-0.8 | 136 | 2.5 | | 0.8-0.9 | 146 | 2.7 | | 0.9-1 | 3242 | 59.7 |
|
GA Branch
GABranch usage summary as of Mon Feb 6 00:01:12 2012
PST.
| Top 10 models used | Distribution of the number of dN/dS classes |
| HKY85 | 2633 | 47.0 | | REV | 576 | 10.3 | | 010000 | 564 | 10.1 | | F81 | 366 | 6.5 | | TRN93 | 233 | 4.2 | | 012012 | 106 | 1.9 | | 001101 | 95 | 1.7 | | 010012 | 52 | 0.9 | | 000010 | 52 | 0.9 | | 010232 | 51 | 0.9 |
|
| 1 | 25 | 0.4 | | 2 | 2281 | 40.7 | | 3 | 1821 | 32.5 | | 4 | 974 | 17.4 | | 5 | 315 | 5.6 | | 6 | 119 | 2.1 | | 7 | 46 | 0.8 | | 8 | 14 | 0.2 | | 9 | 6 | 0.1 |
|
CMS
CMS usage summary as of Mon Feb 6 00:01:15 2012
PST.
| Distribution of mBIC improvement | Number of inferred rate classes |
| 0-10 | 67 | 7.5 | | 10-20 | 32 | 3.6 | | 20-30 | 53 | 5.9 | | 30-40 | 69 | 7.7 | | 40-50 | 79 | 8.8 | | 50-60 | 67 | 7.5 | | 60-70 | 63 | 7.0 | | 70-80 | 41 | 4.6 | | 80-90 | 65 | 7.2 | | 90-100 | 36 | 4.0 | | > 100 | 326 | 36.3 |
|
| 1 | 0 | 0.0 | | 2 | 623 | 69.4 | | 3 | 158 | 17.6 | | 4 | 59 | 6.6 | | 5 | 30 | 3.3 | | 6 | 9 | 1.0 | | 7 | 3 | 0.3 | | 8 | 0 | 0.0 | | 9 | 0 | 0.0 | | ≥ 10 | 16 | 1.8 |
|
DEPS
DEPS usage summary as of Mon Feb 6 00:01:16 2012
PST.
Subtyping
SCUEAL usage summary as of Mon Feb 6 00:01:17 2012
PST.
Top 10 Subtypes (out of 235824 sequences)
| B | 113950 | 48.3 |
| G | 26299 | 11.2 |
| C | 17583 | 7.5 |
| A1 | 11780 | 5.0 |
| Complex | 9690 | 4.1 |
| CRF14 | 8730 | 3.7 |
| F1 | 5516 | 2.3 |
| D | 5061 | 2.1 |
| AE | 3248 | 1.4 |
| B,G recombinant | 3112 | 1.3 |
Coevolution
BGM usage summary as of Mon Feb 6 00:01:19 2012
PST.
Wayne Delport, Art Poon, Simon D.W. Frost and Sergei L. Kosakovsky Pond, 2004-2012