Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Mon Jun 18 00:00:01 2018 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 1 1.00 131 131 131-131 533 533 533-533 48.48 48.48 48.48- 48.48

Last 7 days 68 9.71 31.46 21 3-139 487.54 350 91-2332 5.20 2.56 0.23- 48.48

Last 30 days 451 15.03 38.29 27 3-412 693.75 325 10-9793 10.62 3.61 0.23- 985.61

Lifetime (2766 days) 88001 31.82 51.92 25 3-684 488.45 325 1-11903 21.42 6.22 0.16- 7571.98

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	131	131	131-131	533	533	533-533	48.48	48.48	48.48- 48.48
Last 7 days	68	9.71	31.46	21	3-139	487.54	350	91-2332	5.20	2.56	0.23- 48.48
Last 30 days	451	15.03	38.29	27	3-412	693.75	325	10-9793	10.62	3.61	0.23- 985.61
Lifetime (2766 days)	88001	31.82	51.92	25	3-684	488.45	325	1-11903	21.42	6.22	0.16- 7571.98

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 45520 51.7
TRN93 13111 14.9
REV 9311 10.6
F81 3901 4.4
010230 994 1.1
010232 982 1.1
012212 935 1.1
012012 857 1.0
012232 753 0.9
010000 660 0.7

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 0.6 16.2 73770 83.8
0.05 0.5 14.5 10639 12.1
0.2 0.9 17.3 1291 1.5
0.25 2.3 25.7 727 0.8
0.5 4.4 55.7 616 0.7
0.01 0.8 9.4 522 0.6
0.15 2.8 15.3 92 0.1
0.0024 0.0 2.3 45 0.1
0.3 0.2 20.0 45 0.1
0.0048 0.0 0.5 33 0.0

FEL

FEL usage summary as of Mon Jun 18 00:00:12 2018 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 83 11.86 31.11 16 3-134 559.07 458 95-2022 62.63 35 3-667

Last 30 days 298 9.93 41.45 20 3-476 671.37 404.50 66-3999 104.94 34.50 3-1482

Lifetime (1866 days) 98063 52.55 44.25 24 3-787 479.50 325 1-11276 140.84 44 0-26278

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	83	11.86	31.11	16	3-134	559.07	458	95-2022	62.63	35	3-667
Last 30 days	298	9.93	41.45	20	3-476	671.37	404.50	66-3999	104.94	34.50	3-1482
Lifetime (1866 days)	98063	52.55	44.25	24	3-787	479.50	325	1-11276	140.84	44	0-26278

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 44164 45.0
REV 12892 13.1
TRN93 9661 9.9
F81 4833 4.9
010000 3918 4.0
010232 2032 2.1
012012 1429 1.5
012212 1327 1.4
010230 1201 1.2
012032 942 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.2 79419 81.0
0.05 0.9 19.3 14554 14.8
0.2 2.1 29.0 1953 2.0
0.25 3.2 33.4 850 0.9
0.01 0.4 14.4 486 0.5
0.5 5.4 43.3 196 0.2
0.15 2.8 22.4 136 0.1
0.0024 0.0 7.0 102 0.1
0.3 1.2 22.3 63 0.1
0.0004 0.0 6.6 29 0.0

REL

REL usage summary as of Mon Jun 18 00:00:24 2018 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 31 4.43 15.87 15 3-38 590.90 428 109-1664 166.19 49 1-2286

Last 30 days 130 4.33 14.92 11 3-59 715.82 437.50 66-3551 180.61 53.50 1-2286

Lifetime (1865 days) 54693 29.33 20.60 16 2-110 481.66 319 1-10798 363.38 108 0-39109

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	31	4.43	15.87	15	3-38	590.90	428	109-1664	166.19	49	1-2286
Last 30 days	130	4.33	14.92	11	3-59	715.82	437.50	66-3551	180.61	53.50	1-2286
Lifetime (1865 days)	54693	29.33	20.60	16	2-110	481.66	319	1-10798	363.38	108	0-39109

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 28958 52.9
REV 5579 10.2
TRN93 3206 5.9
F81 3117 5.7
010000 2329 4.3
012012 1072 2.0
001101 720 1.3
010232 683 1.2
012212 667 1.2
012032 559 1.0

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.7 49408 90.3
100 4.2 22.6 1284 2.3
90 19.4 11.1 890 1.6
20 7.3 36.2 808 1.5
10 5.8 32.0 729 1.3
95 2.3 28.0 642 1.2
40 2.5 24.5 144 0.3
80 3.0 28.5 107 0.2
30 10.2 20.6 89 0.2
25 2.5 38.8 80 0.1

TOGGLE

Toggle usage summary as of Mon Jun 18 00:00:30 2018 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 0

Last 30 days 0

Lifetime (2946 days) 1041 0.35 48.35 39 7-150 570.33 346 16-3789 3832.75 2014 31-42841

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	0
Last 30 days	0
Lifetime (2946 days)	1041	0.35	48.35	39	7-150	570.33	346	16-3789	3832.75	2014	31-42841

Model Select.

ModelSelection usage summary as of Mon Jun 18 00:00:31 2018 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 72 10.29 21.54 15 3-134 510.64 375 109-2022

Last 30 days 260 8.67 31.49 15 3-476 520.82 324.50 66-3787

Lifetime (1866 days) 95213 51.03 41.54 22 3-656 515.63 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	72	10.29	21.54	15	3-134	510.64	375	109-2022
Last 30 days	260	8.67	31.49	15	3-476	520.82	324.50	66-3787
Lifetime (1866 days)	95213	51.03	41.54	22	3-656	515.63	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 22868 24.0
TRN93 12572 13.2
F81 8373 8.8
010232 4198 4.4
012012 3123 3.3
012212 2823 3.0
010230 2247 2.4
012032 2179 2.3
012232 2133 2.2
001101 1999 2.1

Model	Times selected	% selected
HKY85	22868	24.0
TRN93	12572	13.2
F81	8373	8.8
010232	4198	4.4
012012	3123	3.3
012212	2823	3.0
010230	2247	2.4
012032	2179	2.3
012232	2133	2.2
001101	1999	2.1

Protein Model Select.

ModelSelectionP usage summary as of Mon Jun 18 00:00:39 2018 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 11 1.57 69.82 44 10-287 1805.45 1101 12-4516

Last 30 days 26 0.87 47.04 37 9-287 1442.27 974.50 12-4516

Lifetime (3667 days) 3760 1.03 45.86 25 2-499 652.68 444 3-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	11	1.57	69.82	44	10-287	1805.45	1101	12-4516
Last 30 days	26	0.87	47.04	37	9-287	1442.27	974.50	12-4516
Lifetime (3667 days)	3760	1.03	45.86	25	2-499	652.68	444	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 549 14.6
JTT (Jones,Taylor,Thornton) 399 10.6
BLOSUM62+F 313 8.3
WAG (Whelan and Goldman)+F 308 8.2
WAG (Whelan and Goldman) 241 6.4
IAV (Influenza A virus)+F 235 6.2
HIV (within host)+F 232 6.2
IAV (Influenza A virus) 216 5.7
BLOSUM62 165 4.4
LG (Le and Gascuel) 159 4.2

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	549	14.6
JTT (Jones,Taylor,Thornton)	399	10.6
BLOSUM62+F	313	8.3
WAG (Whelan and Goldman)+F	308	8.2
WAG (Whelan and Goldman)	241	6.4
IAV (Influenza A virus)+F	235	6.2
HIV (within host)+F	232	6.2
IAV (Influenza A virus)	216	5.7
BLOSUM62	165	4.4
LG (Le and Gascuel)	159	4.2

GARD

GARD usage summary as of Mon Jun 18 00:00:40 2018 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 9 1.29 76.67 42 10-299 3045.56 1262 459-6996 2688.33 3348 99-6308

Last 30 days 87 2.90 33.25 13 3-299 2039.20 772 198-10653 1543.40 222 36-9991

Lifetime (4219 days) 73815 17.50 26.83 18 2-300 2029.89 1110 20-46625 1270.27 374 1-272974

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	9	1.29	76.67	42	10-299	3045.56	1262	459-6996	2688.33	3348	99-6308
Last 30 days	87	2.90	33.25	13	3-299	2039.20	772	198-10653	1543.40	222	36-9991
Lifetime (4219 days)	73815	17.50	26.83	18	2-300	2029.89	1110	20-46625	1270.27	374	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	62126	84.2
HKY85	5991	8.1
010000	860	1.2
REV	830	1.1
TRN93	558	0.8
F81	520	0.7
010232	226	0.3
012212	218	0.3
010230	182	0.2
012232	144	0.2

delta AIC range	Times found	% found
0-10	26798	36.3
10-20	2940	4.0
20-30	2371	3.2
30-40	2212	3.0
40-50	1816	2.5
50-60	1940	2.6
60-70	1399	1.9
70-80	1297	1.8
80-90	1193	1.6
90-100	1068	1.4
> 100	30781	41.7

Number of breakpoints	Times found	% found
0	22514	30.5
1	18720	25.4
2	11693	15.8
3	6769	9.2
4	4113	5.6
5	2846	3.9
6	1849	2.5
7	1403	1.9
8	932	1.3
9	761	1.0
≥ 10	2215	3.0

SBP

SBP usage summary as of Mon Jun 18 00:00:49 2018 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 1 1.00 333 333 333-333 44 44 44-44 8550 8550 8550-8550

Last 7 days 18 2.57 76.89 30 14-340 5.39 1 1-44 1061.94 49 10-8550

Last 30 days 35 1.17 108.63 41 9-427 10.23 1 1-64 1986.60 230 1-15878

Lifetime (1866 days) 20228 10.84 48.64 24 2-656 21.72 1 1-45015 475.16 41 0-279793

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	333	333	333-333	44	44	44-44	8550	8550	8550-8550
Last 7 days	18	2.57	76.89	30	14-340	5.39	1	1-44	1061.94	49	10-8550
Last 30 days	35	1.17	108.63	41	9-427	10.23	1	1-64	1986.60	230	1-15878
Lifetime (1866 days)	20228	10.84	48.64	24	2-656	21.72	1	1-45015	475.16	41	0-279793

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	14524	71.8
REV	1311	6.5
010000	565	2.8
TRN93	501	2.5
F81	500	2.5
0123455	224	1.1
010232	215	1.1
012012	137	0.7
0112304567	115	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	8735	43.2
10-20	889	4.4
20-30	767	3.8
30-40	620	3.1
40-50	504	2.5
50-60	403	2.0
60-70	351	1.7
70-80	372	1.8
80-90	279	1.4
90-100	300	1.5
> 100	7008	34.6

PARRIS

PARRIS usage summary as of Mon Jun 18 00:00:52 2018 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 3 0.43 5.67 4 4-9 614.67 649 546-649 49 9 7-131

Last 30 days 13 0.43 18.15 13 4-37 295.92 66 66-781 266.54 131 7-709

Lifetime (3974 days) 14164 3.56 20.19 15 3-75 484.15 328 7-11903 414.73 136 1-35284

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	3	0.43	5.67	4	4-9	614.67	649	546-649	49	9	7-131
Last 30 days	13	0.43	18.15	13	4-37	295.92	66	66-781	266.54	131	7-709
Lifetime (3974 days)	14164	3.56	20.19	15	3-75	484.15	328	7-11903	414.73	136	1-35284

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	7992	56.4
F81	1054	7.4
REV	996	7.0
TRN93	737	5.2
010000	429	3.0
012012	250	1.8
001101	166	1.2
012212	153	1.1
012032	127	0.9
010230	119	0.8

p-values range	Times found	% found
0-0.1	2601	18.4
0.1-0.2	503	3.6
0.2-0.3	458	3.2
0.3-0.4	361	2.5
0.4-0.5	325	2.3
0.5-0.6	386	2.7
0.6-0.7	363	2.6
0.7-0.8	351	2.5
0.8-0.9	346	2.4
0.9-1	8470	59.8

GA Branch

GABranch usage summary as of Mon Jun 18 00:00:53 2018 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 2 0.29 9 9 4-14 538.50 538.50 428-649 3225 3225 6-6444

Last 30 days 22 0.73 14 11 4-30 769.77 322 58-3999 3266.36 1866 6-9931

Lifetime (3967 days) 11607 2.93 13.73 12 3-30 515.23 329 9-11628 5292.58 1507 1-636439

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	2	0.29	9	9	4-14	538.50	538.50	428-649	3225	3225	6-6444
Last 30 days	22	0.73	14	11	4-30	769.77	322	58-3999	3266.36	1866	6-9931
Lifetime (3967 days)	11607	2.93	13.73	12	3-30	515.23	329	9-11628	5292.58	1507	1-636439

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8340	71.9
REV	613	5.3
010000	568	4.9
F81	414	3.6
TRN93	281	2.4
012012	131	1.1
001101	107	0.9
012212	64	0.6
010012	63	0.5
000010	60	0.5

the number of dN/dS classes range	Times found	% found
1	99	0.9
2	4252	36.6
3	3925	33.8
4	2175	18.7
5	759	6.5
6	228	2.0
7	111	1.0
8	35	0.3
9	23	0.2

CMS

CMS usage summary as of Mon Jun 18 00:00:54 2018 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 2 0.29 15.50 15.50 14-17 966.50 966.50 428-1505 21161 21161 7174-35148

Last 30 days 6 0.20 20.67 19 14-36 630 544.50 192-1505 12040.33 4468.50 1256-35148

Lifetime (3058 days) 3085 1.01 33.82 24 3-120 536.93 335 7-11276 17787.87 3918 59-2971964

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	2	0.29	15.50	15.50	14-17	966.50	966.50	428-1505	21161	21161	7174-35148
Last 30 days	6	0.20	20.67	19	14-36	630	544.50	192-1505	12040.33	4468.50	1256-35148
Lifetime (3058 days)	3085	1.01	33.82	24	3-120	536.93	335	7-11276	17787.87	3918	59-2971964

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
0-10	183	5.9
10-20	142	4.6
20-30	186	6.0
30-40	212	6.9
40-50	239	7.7
50-60	174	5.6
60-70	170	5.5
70-80	126	4.1
80-90	172	5.6
90-100	107	3.5
> 100	1374	44.5

Number of rate classes	Times found	% found
1	0	0.0
2	1964	63.7
3	671	21.8
4	254	8.2
5	101	3.3
6	45	1.5
7	14	0.5
8	2	0.1
9	0	0.0
≥ 10	34	1.1

DEPS

DEPS usage summary as of Mon Jun 18 00:00:55 2018 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 2 0.29 23.50 23.50 10-37 1178 1178 24-2332 304 304 26-582

Last 30 days 8 0.27 19.88 10 9-37 1463.50 2332 12-2332 180.38 27 21-582

Lifetime (2937 days) 2728 0.93 31.94 24 3-100 583.02 435.50 9-11100 434.40 99 2-31585

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	2	0.29	23.50	23.50	10-37	1178	1178	24-2332	304	304	26-582
Last 30 days	8	0.27	19.88	10	9-37	1463.50	2332	12-2332	180.38	27	21-582
Lifetime (2937 days)	2728	0.93	31.94	24	3-100	583.02	435.50	9-11100	434.40	99	2-31585

Subtyping

SCUEAL usage summary as of Mon Jun 18 00:00:56 2018 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 5814 5814.00 82.21 4 0-500

Last 7 days 5814 830.57 82.21 4 0-500

Last 30 days 5814 193.80 82.21 4 0-500

Lifetime (3272 days) 7118 2.18 87.64 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	5814	5814.00	82.21	4	0-500
Last 7 days	5814	830.57	82.21	4	0-500
Last 30 days	5814	193.80	82.21	4	0-500
Lifetime (3272 days)	7118	2.18	87.64	5	0-500

Top 10 Subtypes (out of 623813 sequences)

Subtypes Times found % found

B 242689 38.9

C 107510 17.2

G 44858 7.2

A1 39606 6.3

Complex 25884 4.1

AE 17995 2.9

D 17108 2.7

CRF14 11694 1.9

F1 9791 1.6

B,C recombinant 8113 1.3

Subtypes	Times found	% found
B	242689	38.9
C	107510	17.2
G	44858	7.2
A1	39606	6.3
Complex	25884	4.1
AE	17995	2.9
D	17108	2.7
CRF14	11694	1.9
F1	9791	1.6
B,C recombinant	8113	1.3

Coevolution

BGM usage summary as of Mon Jun 18 00:00:58 2018 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 3 3.00 61.67 65 55-65 0.69 0.67 0.63- 0.75 166.67 147 106-247

Last 7 days 9 1.29 43.67 55 6-65 0.56 0.67 0.09- 0.75 98.33 106 1-259

Last 30 days 13 0.43 40.69 38 6-65 0.83 0.67 0.09- 2.82 77.54 51 1-259

Lifetime (1866 days) 8720 4.67 64.76 30 0-1033 2.26 0.98 0.01-263 2909.62 95.50 0-2900666

Timeframe	Analyses	Sites	Interacting pairs/site	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	3	3.00	61.67	65	55-65	0.69	0.67	0.63- 0.75	166.67	147	106-247
Last 7 days	9	1.29	43.67	55	6-65	0.56	0.67	0.09- 0.75	98.33	106	1-259
Last 30 days	13	0.43	40.69	38	6-65	0.83	0.67	0.09- 2.82	77.54	51	1-259
Lifetime (1866 days)	8720	4.67	64.76	30	0-1033	2.26	0.98	0.01-263	2909.62	95.50	0-2900666

UCSD Viral Evolution Group 2004-2018