Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Fri Sep 3 00:00:00 2010 PST.

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 23 23.00 47.22 21 5-245 397.57 418 23-1063 35.51 13.43 3.35- 256.25

Last 7 days 143 20.43 30.85 11 3-400 407.17 318 23-2964 25.09 5.91 2.46- 304.17

Last 30 days 541 18.03 41.49 19 3-400 384.46 293 10-3863 31.19 11.33 1.79- 510.20

Lifetime (2422 days) 17526 7.24 33.41 20 3-400 365.40 252 2-9794 34.60 14.86 0.95-4721

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	23	23.00	47.22	21	5-245	397.57	418	23-1063	35.51	13.43	3.35- 256.25
Last 7 days	143	20.43	30.85	11	3-400	407.17	318	23-2964	25.09	5.91	2.46- 304.17
Last 30 days	541	18.03	41.49	19	3-400	384.46	293	10-3863	31.19	11.33	1.79- 510.20
Lifetime (2422 days)	17526	7.24	33.41	20	3-400	365.40	252	2-9794	34.60	14.86	0.95-4721

Top 10

Models used Test results by p-value

Model Times Used % Used

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

p-value Selected/100 codons Times Used % Used

Positive Negative

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.

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 19 19.00 45.32 16 5-245 447.11 452 217-1063 138.79 22 5-808

Last 7 days 142 20.29 35.04 19.50 3-245 476.92 452 33-2964 110.95 23 3-1153

Last 30 days 498 16.60 37.04 21 3-245 453.67 363.50 10-4467 95.89 24 1-2213

Lifetime (2073 days) 21542 10.39 30.87 21 3-248 398.26 273 4-9610 135.07 42 0-10979

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	19	19.00	45.32	16	5-245	447.11	452	217-1063	138.79	22	5-808
Last 7 days	142	20.29	35.04	19.50	3-245	476.92	452	33-2964	110.95	23	3-1153
Last 30 days	498	16.60	37.04	21	3-245	453.67	363.50	10-4467	95.89	24	1-2213
Lifetime (2073 days)	21542	10.39	30.87	21	3-248	398.26	273	4-9610	135.07	42	0-10979

Top 10

Models used Test results by p-value

Model Times Used % Used

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

p-value Selected/100 codons Times Used % Used

Positive Negative

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.

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 7 7.00 12.29 12 5-17 350.29 343 217-471 218.14 91 30-1059

Last 7 days 74 10.57 19.68 11 3-71 441.74 363 67-1305 197.50 74.50 7-1231

Last 30 days 299 9.97 19.07 12 3-71 458.62 293 35-3863 267.52 89 1-6007

Lifetime (2073 days) 12771 6.16 17.15 14 2-110 425.21 273 4-9610 442.98 212 0-37794

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	7	7.00	12.29	12	5-17	350.29	343	217-471	218.14	91	30-1059
Last 7 days	74	10.57	19.68	11	3-71	441.74	363	67-1305	197.50	74.50	7-1231
Last 30 days	299	9.97	19.07	12	3-71	458.62	293	35-3863	267.52	89	1-6007
Lifetime (2073 days)	12771	6.16	17.15	14	2-110	425.21	273	4-9610	442.98	212	0-37794

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

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

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

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.

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 1 1.00 16 16 16-16 217 217 217-217 597 597 597-597

Last 7 days 1 0.14 16 16 16-16 217 217 217-217 597 597 597-597

Last 30 days 12 0.40 34.50 24 12-90 220.25 170 69-566 3005 2023.50 204-8534

Lifetime (101 days) 94 0.93 53.80 61.50 7-98 297.43 329 69-568 5196.64 4564 204-26471

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	1	1.00	16	16	16-16	217	217	217-217	597	597	597-597
Last 7 days	1	0.14	16	16	16-16	217	217	217-217	597	597	597-597
Last 30 days	12	0.40	34.50	24	12-90	220.25	170	69-566	3005	2023.50	204-8534
Lifetime (101 days)	94	0.93	53.80	61.50	7-98	297.43	329	69-568	5196.64	4564	204-26471

Model Selection

ModelSelection usage summary as of Fri Sep 3 00:00:36 2010 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 17 17.00 36.47 20 8-137 2278.10 566 102-9710

Last 7 days 133 19.00 32.48 21 3-349 783.63 479 67-9710

Last 30 days 519 17.30 40.92 25 3-349 607.24 399 30-9710

Lifetime (1130 days) 14131 12.51 31.43 20 3-400 460.14 286 4-10000

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	17	17.00	36.47	20	8-137	2278.10	566	102-9710
Last 7 days	133	19.00	32.48	21	3-349	783.63	479	67-9710
Last 30 days	519	17.30	40.92	25	3-349	607.24	399	30-9710
Lifetime (1130 days)	14131	12.51	31.43	20	3-400	460.14	286	4-10000

Top 10 Models

Model Times selected % selected

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

Model	Times selected	% selected
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.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 0

Last 30 days 18 0.60 49.67 32 10-171 409.06 384 73-872

Lifetime (822 days) 404 0.49 42.09 26 2-389 609.19 370 11-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	0
Last 30 days	18	0.60	49.67	32	10-171	409.06	384	73-872
Lifetime (822 days)	404	0.49	42.09	26	2-389	609.19	370	11-18120

Top 10 Models

Model Times selected % selected

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

Model	Times selected	% selected
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.

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 32 32.00 28.19 17.50 4-100 2059.94 699 213-9613 1932.12 1646 1-3757

Last 7 days 105 15.00 22.55 12 4-100 1536.61 417 183-9613 2049.25 2117 1-3757

Last 30 days 432 14.40 26.96 20 3-100 2037.62 1161 133-29130 1227.57 361 1-3757

Lifetime (1374 days) 11862 8.63 19.76 15 2-100 2117.94 1133 57-46625 997.18 251 1-55555

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	32	32.00	28.19	17.50	4-100	2059.94	699	213-9613	1932.12	1646	1-3757
Last 7 days	105	15.00	22.55	12	4-100	1536.61	417	183-9613	2049.25	2117	1-3757
Last 30 days	432	14.40	26.96	20	3-100	2037.62	1161	133-29130	1227.57	361	1-3757
Lifetime (1374 days)	11862	8.63	19.76	15	2-100	2117.94	1133	57-46625	997.18	251	1-55555

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
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

delta AIC range	Times found	% found
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

Number of breakpoints	Times found	% found
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.

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 6 6.00 21.17 16.50 4-63 25.50 16.50 1-77 29 4.50 1-157

Last 7 days 18 2.57 28 22 4-63 29.17 1 1-171 144.83 25.50 1-588

Last 30 days 184 6.13 36.21 24 3-308 13.20 1 1-171 138.36 32 0-2142

Lifetime (1579 days) 5215 3.30 29.70 20 2-328 27.50 1 1-45015 255.94 30 0-129312

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	6	6.00	21.17	16.50	4-63	25.50	16.50	1-77	29	4.50	1-157
Last 7 days	18	2.57	28	22	4-63	29.17	1	1-171	144.83	25.50	1-588
Last 30 days	184	6.13	36.21	24	3-308	13.20	1	1-171	138.36	32	0-2142
Lifetime (1579 days)	5215	3.30	29.70	20	2-328	27.50	1	1-45015	255.94	30	0-129312

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
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

IC improvement range	Times found	% found
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.

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 8 8.00 20.38 18 5-55 355.62 362 217-471 91.38 64 31-221

Last 7 days 38 5.43 19.71 11.50 5-55 441.58 365 113-992 1000.92 67 7-14391

Last 30 days 109 3.63 22.17 16 5-71 489.19 350 82-2584 827.94 159 7-14391

Lifetime (1129 days) 3188 2.82 18.76 16 3-75 433.54 317 11-8871 456.77 194 1-16085

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	8	8.00	20.38	18	5-55	355.62	362	217-471	91.38	64	31-221
Last 7 days	38	5.43	19.71	11.50	5-55	441.58	365	113-992	1000.92	67	7-14391
Last 30 days	109	3.63	22.17	16	5-71	489.19	350	82-2584	827.94	159	7-14391
Lifetime (1129 days)	3188	2.82	18.76	16	3-75	433.54	317	11-8871	456.77	194	1-16085

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
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

p-values range	Times found	% found
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.

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 1 1.00 16 16 16-16 217 217 217-217 706 706 706-706

Last 7 days 12 1.71 15.17 15.50 4-26 427 285 139-1257 4083.25 2240.50 8-22908

Last 30 days 51 1.70 17.43 19 4-30 313.82 217 31-1439 3929.98 1834 8-27868

Lifetime (1122 days) 3441 3.07 14.29 13 3-30 476.59 285 14-10000 5914.42 2047 1-253122

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	1	1.00	16	16	16-16	217	217	217-217	706	706	706-706
Last 7 days	12	1.71	15.17	15.50	4-26	427	285	139-1257	4083.25	2240.50	8-22908
Last 30 days	51	1.70	17.43	19	4-30	313.82	217	31-1439	3929.98	1834	8-27868
Lifetime (1122 days)	3441	3.07	14.29	13	3-30	476.59	285	14-10000	5914.42	2047	1-253122

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
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

the number of dN/dS classes range	Times found	% found
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.

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 1 1.00 16 16 16-16 217 217 217-217 1187 1187 1187-1187

Last 7 days 6 0.86 35.33 46 12-46 356 332 145-555 7682.50 6509.50 1187-20230

Last 30 days 32 1.07 41.09 40.50 11-99 314.28 234.50 47-1248 10207.66 6106 1108-48396

Lifetime (213 days) 292 1.37 32.64 28 3-99 387.07 252 7-3965 12823.55 3822.50 71-416053

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	1	1.00	16	16	16-16	217	217	217-217	1187	1187	1187-1187
Last 7 days	6	0.86	35.33	46	12-46	356	332	145-555	7682.50	6509.50	1187-20230
Last 30 days	32	1.07	41.09	40.50	11-99	314.28	234.50	47-1248	10207.66	6106	1108-48396
Lifetime (213 days)	292	1.37	32.64	28	3-99	387.07	252	7-3965	12823.55	3822.50	71-416053

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
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

Number of rate classes	Times found	% found
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.

Timeframe Analyses Sequences Sites CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 1 1.00 43 43 43-43 471 471 471-471 648 648 648-648

Last 7 days 1 0.14 43 43 43-43 471 471 471-471 648 648 648-648

Last 30 days 13 0.43 28.92 22 10-79 388.69 418 72-872 249.62 63 12-1061

Lifetime (92 days) 46 0.50 34.22 35 3-79 321.93 329 36-872 194 130.50 5-1061

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	1	1.00	43	43	43-43	471	471	471-471	648	648	648-648
Last 7 days	1	0.14	43	43	43-43	471	471	471-471	648	648	648-648
Last 30 days	13	0.43	28.92	22	10-79	388.69	418	72-872	249.62	63	12-1061
Lifetime (92 days)	46	0.50	34.22	35	3-79	321.93	329	36-872	194	130.50	5-1061

Co-evolution

BGM usage summary as of Fri Sep 3 00:01:00 2010 PST.

Timeframe Analyses Sites Interacting pairs/site CPU time

Total Per 24 hrs Mean Median Range Mean Median Range Mean Median Range

Last 1 days 1 1.00 25 25 25-25 0.64 0.64 0.64- 0.64 11 11 11-11

Last 7 days 5 0.71 163 39 17-638 0.45 0.54 0.08- 0.88 88 11 3-393

Last 30 days 52 1.73 102.90 27.50 3-727 1.20 0.65 0.05- 7.62 564.10 33.50 0-15383

Lifetime (903 days) 2164 2.40 57.26 33 1-727 2.05 0.94 0.02- 58.76 2030.17 180.50 0-1103550

Timeframe	Analyses	Sites	Interacting pairs/site	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	1	1.00	25	25	25-25	0.64	0.64	0.64- 0.64	11	11	11-11
Last 7 days	5	0.71	163	39	17-638	0.45	0.54	0.08- 0.88	88	11	3-393
Last 30 days	52	1.73	102.90	27.50	3-727	1.20	0.65	0.05- 7.62	564.10	33.50	0-15383
Lifetime (903 days)	2164	2.40	57.26	33	1-727	2.05	0.94	0.02- 58.76	2030.17	180.50	0-1103550

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