Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Mon Feb 6 00:00:01 2012 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 42 42.00 72.38 32.50 3-485 597.57 320.50 123-3433 45.11 10.26 1.79- 451.98

Last 7 days 255 36.43 55.33 23 3-500 493.09 315 65-3433 36.79 11.61 1.79- 610.08

Last 30 days 960 32.00 63.10 26 3-500 470.69 326 19-4136 39.41 11.53 1.11- 933.95

Lifetime (111 days) 3390 30.54 46.74 21 3-500 480.45 326 4-4420 30.31 11.19 1.11-1251

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	42	42.00	72.38	32.50	3-485	597.57	320.50	123-3433	45.11	10.26	1.79- 451.98
Last 7 days	255	36.43	55.33	23	3-500	493.09	315	65-3433	36.79	11.61	1.79- 610.08
Last 30 days	960	32.00	63.10	26	3-500	470.69	326	19-4136	39.41	11.53	1.11- 933.95
Lifetime (111 days)	3390	30.54	46.74	21	3-500	480.45	326	4-4420	30.31	11.19	1.11-1251

Top 10

Models used Test results by p-value

Model Times Used % Used

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

p-value Selected/100 codons Times Used % Used

Positive Negative

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.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 39 39.00 71.41 14 4-485 1099.77 352 160-3433 341.59 45 1-3818

Last 7 days 279 39.86 45.09 16 3-500 565.08 328 23-3433 147.36 34 1-4609

Last 30 days 865 28.83 59.42 22 3-500 453.39 312 23-3433 140.69 35 1-4889

Lifetime (2594 days) 33577 12.94 35.95 22 3-500 420.09 290 4-10166 132.67 37 0-23196

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	39	39.00	71.41	14	4-485	1099.77	352	160-3433	341.59	45	1-3818
Last 7 days	279	39.86	45.09	16	3-500	565.08	328	23-3433	147.36	34	1-4609
Last 30 days	865	28.83	59.42	22	3-500	453.39	312	23-3433	140.69	35	1-4889
Lifetime (2594 days)	33577	12.94	35.95	22	3-500	420.09	290	4-10166	132.67	37	0-23196

Top 10

Models used Test results by p-value

Model Times Used % Used

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

p-value Selected/100 codons Times Used % Used

Positive Negative

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.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 11 11.00 11 5 4-56 852.91 312 122-3433 182.18 14 4-1265

Last 7 days 153 21.86 19.82 14 4-73 520.99 312 26-3433 286.98 65 4-5268

Last 30 days 483 16.10 19.82 15 3-73 494.77 312 20-3433 240.15 49 1-5346

Lifetime (2594 days) 21284 8.21 18.26 14 2-110 432.98 288 4-10166 371.13 137 0-37794

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	11	11.00	11	5	4-56	852.91	312	122-3433	182.18	14	4-1265
Last 7 days	153	21.86	19.82	14	4-73	520.99	312	26-3433	286.98	65	4-5268
Last 30 days	483	16.10	19.82	15	3-73	494.77	312	20-3433	240.15	49	1-5346
Lifetime (2594 days)	21284	8.21	18.26	14	2-110	432.98	288	4-10166	371.13	137	0-37794

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

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

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

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.

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 69 69 69-69 226 226 226-226 3802 3802 3802-3802

Last 7 days 4 0.57 52 59.50 20-69 205.75 209.50 178-226 2193 2049.50 871-3802

Last 30 days 9 0.30 38.22 36 15-69 337 296 178-493 2670 2363 871-4844

Lifetime (622 days) 320 0.51 44.51 34.50 7-144 464.94 329 36-3478 4331.52 2672 46-26471

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	69	69	69-69	226	226	226-226	3802	3802	3802-3802
Last 7 days	4	0.57	52	59.50	20-69	205.75	209.50	178-226	2193	2049.50	871-3802
Last 30 days	9	0.30	38.22	36	15-69	337	296	178-493	2670	2363	871-4844
Lifetime (622 days)	320	0.51	44.51	34.50	7-144	464.94	329	36-3478	4331.52	2672	46-26471

Model Select.

ModelSelection usage summary as of Mon Feb 6 00:00:39 2012 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 10 10.00 27 14 8-93 437.60 309 148-1342

Last 7 days 214 30.57 31.52 21 3-316 445.29 317.50 23- 3824.67

Last 30 days 798 26.60 41.54 21 3-466 432.16 300 18.33-4136

Lifetime (1651 days) 25560 15.48 34.61 20 3-500 487.13 314 4-10166

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	10	10.00	27	14	8-93	437.60	309	148-1342
Last 7 days	214	30.57	31.52	21	3-316	445.29	317.50	23- 3824.67
Last 30 days	798	26.60	41.54	21	3-466	432.16	300	18.33-4136
Lifetime (1651 days)	25560	15.48	34.61	20	3-500	487.13	314	4-10166

Top 10 Models

Model Times selected % selected

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

Model	Times selected	% selected
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.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 10 1.43 36.40 22 9-131 538.10 566 257-877

Last 30 days 24 0.80 44.17 21.50 8-353 552.88 501 195-2109

Lifetime (1343 days) 908 0.68 44.56 27 2-389 619.20 399 3-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	10	1.43	36.40	22	9-131	538.10	566	257-877
Last 30 days	24	0.80	44.17	21.50	8-353	552.88	501	195-2109
Lifetime (1343 days)	908	0.68	44.56	27	2-389	619.20	399	3-18120

Top 10 Models

Model Times selected % selected

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

Model	Times selected	% selected
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.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 2 2.00 30.50 30.50 21-40 1150.50 1150.50 603-1698 227 227 56-398

Last 7 days 81 11.57 27.35 20 4-89 1674.59 1059 129-11474 976.40 372 13-6389

Last 30 days 342 11.40 23.38 16 3-100 1556.69 1207.50 92-11648 997.88 293 8-9456

Lifetime (1895 days) 18339 9.68 21.84 16 2-100 2004.36 1086 22-46625 1026.81 262 1-55555

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	2	2.00	30.50	30.50	21-40	1150.50	1150.50	603-1698	227	227	56-398
Last 7 days	81	11.57	27.35	20	4-89	1674.59	1059	129-11474	976.40	372	13-6389
Last 30 days	342	11.40	23.38	16	3-100	1556.69	1207.50	92-11648	997.88	293	8-9456
Lifetime (1895 days)	18339	9.68	21.84	16	2-100	2004.36	1086	22-46625	1026.81	262	1-55555

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
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

delta AIC range	Times found	% found
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

Number of breakpoints	Times found	% found
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.

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 9.67 9 6-17 186.50 2 1-843 56.33 19 0-230

Last 7 days 82 11.71 26.62 10 4-316 47.80 1.50 1-843 105.52 9 0-2451

Last 30 days 255 8.50 30.62 12 3-388 21.95 1 1-843 130.22 6 0-3024

Lifetime (2100 days) 8074 3.84 37.42 23 2-491 22.28 1 1-45015 295.81 33 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	9.67	9	6-17	186.50	2	1-843	56.33	19	0-230
Last 7 days	82	11.71	26.62	10	4-316	47.80	1.50	1-843	105.52	9	0-2451
Last 30 days	255	8.50	30.62	12	3-388	21.95	1	1-843	130.22	6	0-3024
Lifetime (2100 days)	8074	3.84	37.42	23	2-491	22.28	1	1-45015	295.81	33	0-129312

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
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

IC improvement range	Times found	% found
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.

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 56 56 56-56 3433 3433 3433-3433 1106 1106 1106-1106

Last 7 days 36 5.14 27.56 21.50 4-73 635.97 386 65-3433 191.89 139 7-1106

Last 30 days 137 4.57 22.96 17 4-73 622.01 361 65-3434 165.18 114 4-2330

Lifetime (1650 days) 5434 3.29 19.14 14 3-75 470.92 333 9-8871 418.04 153 1-16085

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	56	56	56-56	3433	3433	3433-3433	1106	1106	1106-1106
Last 7 days	36	5.14	27.56	21.50	4-73	635.97	386	65-3433	191.89	139	7-1106
Last 30 days	137	4.57	22.96	17	4-73	622.01	361	65-3434	165.18	114	4-2330
Lifetime (1650 days)	5434	3.29	19.14	14	3-75	470.92	333	9-8871	418.04	153	1-16085

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
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

p-values range	Times found	% found
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.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 3 3.00 22.33 21 21-25 597.67 566 566-661 13131.67 8011 5820-25564

Last 7 days 69 9.86 9.22 5 3-25 333.96 172 43-3276 1847.71 29 2-25564

Last 30 days 162 5.40 13.76 13 3-30 477.38 244.50 26-3639 3853.49 796.50 2-67834

Lifetime (1643 days) 5601 3.41 13.68 12 3-30 464.25 295 10-10000 5410.92 1584 1-253122

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	3	3.00	22.33	21	21-25	597.67	566	566-661	13131.67	8011	5820-25564
Last 7 days	69	9.86	9.22	5	3-25	333.96	172	43-3276	1847.71	29	2-25564
Last 30 days	162	5.40	13.76	13	3-30	477.38	244.50	26-3639	3853.49	796.50	2-67834
Lifetime (1643 days)	5601	3.41	13.68	12	3-30	464.25	295	10-10000	5410.92	1584	1-253122

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
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

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

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 56 56 56-56 3433 3433 3433-3433 11091 11091 11091-11091

Last 7 days 16 2.29 29.75 24 9-57 1027.44 560 66-3433 23953.94 10798.50 370-101216

Last 30 days 50 1.67 26.94 21.50 5-68 668.60 370 17-3434 11804.42 2269 370-101216

Lifetime (734 days) 898 1.22 30.16 22 3-118 458.25 303.50 7-10166 13706.83 3189.50 71-1500725

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	56	56	56-56	3433	3433	3433-3433	11091	11091	11091-11091
Last 7 days	16	2.29	29.75	24	9-57	1027.44	560	66-3433	23953.94	10798.50	370-101216
Last 30 days	50	1.67	26.94	21.50	5-68	668.60	370	17-3434	11804.42	2269	370-101216
Lifetime (734 days)	898	1.22	30.16	22	3-118	458.25	303.50	7-10166	13706.83	3189.50	71-1500725

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
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

Number of rate classes	Times found	% found
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.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 0

Last 7 days 10 1.43 27.10 22 21-39 574.30 566 285-930 79.90 64 52-123

Last 30 days 23 0.77 22.83 21 8-51 576 517 163-2109 119.09 57 9-739

Lifetime (613 days) 561 0.92 27.83 21 3-100 423.80 300 34-3434 163.58 49 2-5105

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	10	1.43	27.10	22	21-39	574.30	566	285-930	79.90	64	52-123
Last 30 days	23	0.77	22.83	21	8-51	576	517	163-2109	119.09	57	9-739
Lifetime (613 days)	561	0.92	27.83	21	3-100	423.80	300	34-3434	163.58	49	2-5105

Subtyping

SCUEAL usage summary as of Mon Feb 6 00:01:17 2012 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 639 639.00 140.89 9 0-500

Last 7 days 639 91.29 140.89 9 0-500

Last 30 days 639 21.30 140.89 9 0-500

Lifetime (945 days) 1942 2.06 121.43 13 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	639	639.00	140.89	9	0-500
Last 7 days	639	91.29	140.89	9	0-500
Last 30 days	639	21.30	140.89	9	0-500
Lifetime (945 days)	1942	2.06	121.43	13	0-500

Top 10 Subtypes (out of 235824 sequences)

Subtypes Times found % found

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

Subtypes	Times found	% found
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.

Timeframe Analyses Sites Interacting pairs/site CPU time

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

Last 1 days 0

Last 7 days 17 2.43 38.65 35 5-105 2.97 1.20 0.11-15 574 80 1-2497

Last 30 days 103 3.43 44.50 28 1-280 2.32 1.21 0.11-20 462.52 87 0-3465

Lifetime (1424 days) 3651 2.56 67.26 34 1-964 2.12 0.90 0.01-214 1547.75 147 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	0
Last 7 days	17	2.43	38.65	35	5-105	2.97	1.20	0.11-15	574	80	1-2497
Last 30 days	103	3.43	44.50	28	1-280	2.32	1.21	0.11-20	462.52	87	0-3465
Lifetime (1424 days)	3651	2.56	67.26	34	1-964	2.12	0.90	0.01-214	1547.75	147	0-1103550

Wayne Delport, Art Poon, Simon D.W. Frost and Sergei L. Kosakovsky Pond, 2004-2012