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SLAC

SLAC usage summary as of Wed Mar 10 00:00:01 2010 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days41 41.00 24.68168-148 370.0227553-1921 16.63 10.68 3.35- 79.84
Last 7 days182 26.00 25.92 15.504-163404 320.5053-2978 17.75 11.16 1.60- 192.10
Last 30 days721 24.03 31.88223-245 418.8126315-3965 33.51 8.62 0.95- 2938.17
Lifetime (2245 days)13922 6.20 30.99193-247 348.072322-9794 35.82 15.29 0.95-4721

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY857569 54.4
REV1687 12.1
0100001589 11.4
F81465 3.3
TRN93402 2.9
012212215 1.5
001101149 1.1
012012122 0.9
000010110 0.8
01023290 0.6
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 12.110857 78.0
0.05 1.0 7.52383 17.1
0.25 1.2 36.1198 1.4
0.2 1.0 27.8140 1.0
0.5 5.5 27.898 0.7
0.3 1.2 26.177 0.6
0.01 1.1 6.662 0.4
0.9 23.6 53.230 0.2
0.15 2.5 32.417 0.1
0.06 0.3 6.210 0.1

FEL

FEL usage summary as of Wed Mar 10 00:00:10 2010 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days19 19.00 28.95226-78 321.74249108-886 58.32383-197
Last 7 days157 22.43 41.39264-196 415.9936663-2472 75.33331-838
Last 30 days633 21.10 30.75213-197 416.4424815-3965 63.47221-2778
Lifetime (1896 days)18053 9.52 29.32213-200 394.112624-9528 139.18450-10979

Top 10

Models usedTest results by p-value
ModelTimes Used% Used
HKY857236 40.1
REV2947 16.3
0100002259 12.5
F81742 4.1
TRN93709 3.9
012212325 1.8
000010251 1.4
001101227 1.3
010232216 1.2
012012204 1.1
p-valueSelected/100 codonsTimes Used% Used
PositiveNegative
0.1 1.1 20.414762 81.8
0.05 0.9 14.62475 13.7
0.2 2.1 15.5280 1.6
0.25 3.1 35.5231 1.3
0.5 5.2 39.770 0.4
0.01 0.4 17.967 0.4
0.15 1.4 15.042 0.2
0.19 0.2 4.514 0.1
0.3 1.9 11.912 0.1
0.06 0.8 10.611 0.1

REL

REL usage summary as of Wed Mar 10 00:00:23 2010 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days16 16.00 23.44236-50322262108-886 265.75 284.5036-495
Last 7 days113 16.14 21.86194-62 370.4731672-2472 214.1211012-3110
Last 30 days522 17.40 16.52 11.503-74 401.2226315-3965 313.441011-21574
Lifetime (1896 days)10663 5.62 16.28142-110 420.492674-9528 475.442410-37794

Top 10

Models usedTest results by Bayes Factor
ModelTimes Used% Used
HKY854691 44.0
0100001521 14.3
REV1279 12.0
F81471 4.4
TRN93459 4.3
012012176 1.7
012212153 1.4
001101132 1.2
010232110 1.0
000010102 1.0
Bayes FactorSelected/100 codonsTimes Used% Used
PositiveNegative
50 4.0 22.68893 83.4
10 5.9 34.1408 3.8
90 30.5 3.7400 3.8
100 2.9 22.2337 3.2
20 9.6 34.0325 3.0
95 3.1 21.696 0.9
40 6.7 15.550 0.5
0.1 53.1 84.347 0.4
30 2.9 25.333 0.3
5 12.3 21.916 0.2

Model Selection

ModelSelection usage summary as of Wed Mar 10 00:00:29 2010 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days31 31.00 20.42226-78 625.3231753-1969
Last 7 days137 19.57 20.36144-78 573.8232353-3184
Last 30 days645 21.50 28.47163-241 437.1124415-3965
Lifetime (953 days)10794 11.33 29.76193-250 445.742684-10000

Top 10 Models

ModelTimes selected% selected
HKY853408 31.6
F811023 9.5
TRN93654 6.1
012212447 4.1
010232338 3.1
012232283 2.6
012012278 2.6
000010276 2.6
001101270 2.5
010230245 2.3

Protein Model Selection

ModelSelectionP usage summary as of Wed Mar 10 00:00:35 2010 PST.

TimeframeAnalysesSequencesSites
TotalPer 24 hrsMeanMedianRangeMeanMedianRange
Last 1 days0
Last 7 days1 0.14565656-56606060-60
Last 30 days11 0.37 71.73485-244144117360-6578
Lifetime (645 days)291 0.45 38.57242-244 680.4241235-18120

Top 10 Models

ModelTimes selected% selected
JTT (Jones,Taylor,Thornton)71 24.4
WAG (Whelan and Goldman)53 18.2
LG (Le and Gascuel)48 16.5
HIV (between hosts)39 13.4
BLOSUM6226 8.9
HIV (within host)19 6.5
Dayhoff10 3.4
IAV (Influenza A virus)8 2.7
VT (Vingron and Muller)6 2.1
rtREV (reverse transcriptase)5 1.7

GARD

GARD usage summary as of Wed Mar 10 00:00:35 2010 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days28 28.00 22.79186-9810691053324-3198 560.93991-3029
Last 7 days89 12.71 25.62163-98 1957.981116216-9981 775.332531-3774
Last 30 days544 18.13 23.70183-100 1369.54109560-9981 968.172221-3939
Lifetime (1197 days)9467 7.91 18.89152-100 2180.73114657-46625 1051.582891-55555

Top 10 models usedDistribution of delta AICNumber of inferred breakpoints
ModelTimes Used% Used
03623 38.3
HKY852995 31.6
010000430 4.5
REV415 4.4
TRN93279 2.9
F81260 2.7
010232113 1.2
012212109 1.2
01023091 1.0
01223272 0.8
delta AIC rangeTimes found% found
0-102797 29.5
10-20439 4.6
20-30372 3.9
30-40326 3.4
40-50278 2.9
50-60257 2.7
60-70199 2.1
70-80157 1.7
80-90157 1.7
90-100124 1.3
> 1004361 46.1
Number of breakpointsTimes found% found
02165 22.9
12277 24.1
21674 17.7
31051 11.1
4661 7.0
5462 4.9
6307 3.2
7215 2.3
8133 1.4
9126 1.3
≥ 10396 4.2

SBP

SBP usage summary as of Wed Mar 10 00:00:42 2010 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days11 11.0040106-120 6.1811-46 231.91164-1220
Last 7 days38 5.43 49.13 22.506-250 7.9531-46 370.84 24.501-6041
Last 30 days158 5.27 36.80165-250 6.0311-62 148.83140-6041
Lifetime (1402 days)4413 3.15 26.04192-250 30.0311-45015 241.40280-129312

Top 10 models usedDistribution of IC improvement
ModelTimes Used% Used
HKY852117 48.0
REV515 11.7
010000316 7.2
F81241 5.5
TRN93209 4.7
010232115 2.6
01221262 1.4
01223256 1.3
00001050 1.1
01021247 1.1
IC improvement rangeTimes found% found
0-101710 38.7
10-20219 5.0
20-30196 4.4
30-40139 3.1
40-50128 2.9
50-6092 2.1
60-7078 1.8
70-8076 1.7
80-9056 1.3
90-10056 1.3
> 1001663 37.7

PARRIS

PARRIS usage summary as of Wed Mar 10 00:00:46 2010 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days2 2.00 18.50 18.509-28408408211-605696948-90
Last 7 days41 5.86 20.83155-62 294.1726572-947 303.209010-3981
Last 30 days146 4.87 16.66113-74 394.29 342.5027-1717 242.55833-4667
Lifetime (952 days)2551 2.68 17.53163-74 429.0430011-6061 436.872051-10666

Top 10 models usedDistribution of p-values
ModelTimes Used% Used
HKY851238 48.5
010000256 10.0
REV215 8.4
F81129 5.1
TRN93115 4.5
01221265 2.5
01201244 1.7
01203032 1.3
01223230 1.2
00001025 1.0
p-values rangeTimes found% found
0-0.1474 18.6
0.1-0.296 3.8
0.2-0.3102 4.0
0.3-0.457 2.2
0.4-0.580 3.1
0.5-0.663 2.5
0.6-0.753 2.1
0.7-0.875 2.9
0.8-0.973 2.9
0.9-11478 57.9

GA Branch

GABranch usage summary as of Wed Mar 10 00:00:47 2010 PST.

TimeframeAnalysesSequencesSitesCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days4 4.00 24.502422-28 210.75230108-275 4161.25 4405.502818-5016
Last 7 days31 4.43 15.03144-30 323.9029763-1288297321115-12074
Last 30 days161 5.37 13.30114-30 366.3432757-1288 4001.4313205-33721
Lifetime (945 days)2653 2.81 14.60143-30 485.3228314-10000 6378.8621102-253122

Top 10 models usedDistribution of the number of dN/dS classes
ModelTimes Used% Used
HKY851242 46.8
REV331 12.5
010000321 12.1
F8186 3.2
TRN9383 3.1
01201244 1.7
01223234 1.3
00001031 1.2
00110127 1.0
01203226 1.0
the number of dN/dS classes rangeTimes found% found
14 0.2
2912 34.4
3958 36.1
4519 19.6
5163 6.1
662 2.3
726 1.0
89 0.3
90 0.0

Co-evolution

BGM usage summary as of Wed Mar 10 00:00:49 2010 PST.

TimeframeAnalysesSitesInteracting pairs/siteCPU time
TotalPer 24 hrsMeanMedianRangeMeanMedianRangeMeanMedianRange
Last 1 days9 9.00 33.332610-119 2.42 1.75 1.11- 6.50 197.788424-675
Last 7 days41 5.86 48.78267-237 1.69 1.13 0.13- 6.71 183.80961-675
Last 30 days93 3.10 60.40286-354 1.19 0.83 0.09- 6.71 252.12600-4383
Lifetime (726 days)1768 2.44 53.75 31.501-482 2.20 0.97 0.02- 58.76 2235.00 209.500-1103550

Sergei L. Kosakovsky Pond, Art Poon, Wayne Delport and Simon D.W. Frost, 2004-2010