Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Fri Dec 4 00:00:01 2020 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 (3666 days) 92479 25.23 53.07 25 3-684 490.95 325 1-11903 21.25 6.16 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	0
Last 7 days	0
Last 30 days	0
Lifetime (3666 days)	92479	25.23	53.07	25	3-684	490.95	325	1-11903	21.25	6.16	0.16- 7571.98

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 47511 51.4
TRN93 13462 14.6
REV 9543 10.3
F81 4265 4.6
010230 1079 1.2
012012 1076 1.2
012212 1060 1.1
010232 1010 1.1
012232 856 0.9
012032 760 0.8

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 0.6 16.2 77137 83.4
0.05 0.5 14.1 11486 12.4
0.2 0.9 18.4 1381 1.5
0.25 2.2 24.8 776 0.8
0.5 4.3 55.2 659 0.7
0.01 0.8 9.6 540 0.6
0.15 2.2 15.2 115 0.1
0.3 0.2 18.1 51 0.1
0.0024 0.0 2.3 45 0.0
0.0048 0.0 0.5 33 0.0

FEL

FEL usage summary as of Fri Dec 4 00:01:05 2020 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 41.27 30 16-168 3485.64 3958 1353-3958 714.45 753 26-1006

Last 7 days 24 3.43 43.29 30 5-168 2497.04 1996.50 251-3958 578.79 589 6-1782

Last 30 days 64 2.13 47.47 30 4-275 1549.05 854 87-9740 303.78 98 5-2062

Lifetime (2766 days) 103701 37.49 44.50 24 3-787 487.72 325 1-11276 181.59 46 0-51470

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	41.27	30	16-168	3485.64	3958	1353-3958	714.45	753	26-1006
Last 7 days	24	3.43	43.29	30	5-168	2497.04	1996.50	251-3958	578.79	589	6-1782
Last 30 days	64	2.13	47.47	30	4-275	1549.05	854	87-9740	303.78	98	5-2062
Lifetime (2766 days)	103701	37.49	44.50	24	3-787	487.72	325	1-11276	181.59	46	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 47130 45.4
REV 13314 12.8
TRN93 10140 9.8
F81 5402 5.2
010000 3929 3.8
010232 2094 2.0
012012 1582 1.5
012212 1402 1.4
010230 1269 1.2
012032 1005 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.0 83839 80.8
0.05 0.9 19.1 15342 14.8
0.2 2.1 29.7 2136 2.1
0.25 3.1 31.9 942 0.9
0.01 0.4 14.7 523 0.5
0.5 5.9 43.2 214 0.2
0.15 2.3 22.7 181 0.2
0.0024 0.0 7.0 102 0.1
0.3 1.2 23.3 64 0.1
0.06 0.3 22.5 60 0.1

REL

REL usage summary as of Fri Dec 4 00:01:46 2020 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 28.25 30 16-30 3632.38 3958 1353-3958 1160.50 1245.50 57-1721

Last 7 days 21 3.00 25.43 30 5-38 2253 1353 251-3958 709.24 359 3-2303

Last 30 days 85 2.83 25 24 5-62 1115.85 763 89-9740 291.01 110 3-2303

Lifetime (2765 days) 58037 20.99 20.71 16 2-110 488.14 323 1-11542 390.37 111 0-54132

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	28.25	30	16-30	3632.38	3958	1353-3958	1160.50	1245.50	57-1721
Last 7 days	21	3.00	25.43	30	5-38	2253	1353	251-3958	709.24	359	3-2303
Last 30 days	85	2.83	25	24	5-62	1115.85	763	89-9740	291.01	110	3-2303
Lifetime (2765 days)	58037	20.99	20.71	16	2-110	488.14	323	1-11542	390.37	111	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 30855 53.2
REV 5698 9.8
F81 3525 6.1
TRN93 3362 5.8
010000 2344 4.0
012012 1223 2.1
001101 730 1.3
012212 718 1.2
010232 709 1.2
012032 619 1.1

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.8 52462 90.4
100 4.4 22.1 1318 2.3
90 19.2 11.2 901 1.6
20 7.2 35.9 824 1.4
95 2.4 31.6 764 1.3
10 5.8 31.9 747 1.3
40 2.5 24.4 145 0.2
25 7.8 34.7 115 0.2
80 3.0 28.4 110 0.2
30 9.8 20.6 93 0.2

TOGGLE

Toggle usage summary as of Fri Dec 4 00:01:57 2020 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 1 0.14 23 23 23-23 503 503 503-503 1591 1591 1591-1591

Last 30 days 1 0.03 23 23 23-23 503 503 503-503 1591 1591 1591-1591

Lifetime (3846 days) 1091 0.28 47.56 37 7-150 569.20 350 16-3789 3767.81 1973 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	1	0.14	23	23	23-23	503	503	503-503	1591	1591	1591-1591
Last 30 days	1	0.03	23	23	23-23	503	503	503-503	1591	1591	1591-1591
Lifetime (3846 days)	1091	0.28	47.56	37	7-150	569.20	350	16-3789	3767.81	1973	31-42841

Model Select.

ModelSelection usage summary as of Fri Dec 4 00:01:59 2020 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 20 20.00 30.65 30 7-55 538.10 518 133-1008

Last 7 days 39 5.57 45.74 29 7-330 550.28 503 54-2466

Last 30 days 126 4.20 35.65 23 4-330 759.20 514 54-9740

Lifetime (2766 days) 102346 37.00 43.81 22 3-656 522.47 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	20	20.00	30.65	30	7-55	538.10	518	133-1008
Last 7 days	39	5.57	45.74	29	7-330	550.28	503	54-2466
Last 30 days	126	4.20	35.65	23	4-330	759.20	514	54-9740
Lifetime (2766 days)	102346	37.00	43.81	22	3-656	522.47	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24570 24.0
TRN93 13096 12.8
F81 8884 8.7
010232 4379 4.3
012012 3587 3.5
012212 3087 3.0
010230 2483 2.4
012232 2434 2.4
012032 2430 2.4
001101 2114 2.1

Model	Times selected	% selected
HKY85	24570	24.0
TRN93	13096	12.8
F81	8884	8.7
010232	4379	4.3
012012	3587	3.5
012212	3087	3.0
010230	2483	2.4
012232	2434	2.4
012032	2430	2.4
001101	2114	2.1

Protein Model Select.

ModelSelectionP usage summary as of Fri Dec 4 00:02:14 2020 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 1 0.03 15 15 15-15 9942 9942 9942-9942

Lifetime (4567 days) 3945 0.86 46.55 25 2-500 674.71 444 3-18120

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	1	0.03	15	15	15-15	9942	9942	9942-9942
Lifetime (4567 days)	3945	0.86	46.55	25	2-500	674.71	444	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 567 14.4
JTT (Jones,Taylor,Thornton) 410 10.4
BLOSUM62+F 327 8.3
WAG (Whelan and Goldman)+F 325 8.2
HIV (within host)+F 272 6.9
WAG (Whelan and Goldman) 245 6.2
IAV (Influenza A virus)+F 243 6.2
IAV (Influenza A virus) 228 5.8
BLOSUM62 169 4.3
LG (Le and Gascuel) 168 4.3

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	567	14.4
JTT (Jones,Taylor,Thornton)	410	10.4
BLOSUM62+F	327	8.3
WAG (Whelan and Goldman)+F	325	8.2
HIV (within host)+F	272	6.9
WAG (Whelan and Goldman)	245	6.2
IAV (Influenza A virus)+F	243	6.2
IAV (Influenza A virus)	228	5.8
BLOSUM62	169	4.3
LG (Le and Gascuel)	168	4.3

GARD

GARD usage summary as of Fri Dec 4 00:02:16 2020 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 4 4.00 32.75 36 23-36 1555.50 1941 399-1941 2973.75 3782.50 437-3893

Last 7 days 18 2.57 30.94 23 7-101 2270.50 1173 399-11874 2158.06 2437 120-3893

Last 30 days 69 2.30 27.94 21 5-190 4719.07 1413 360-29220 1384.23 872 44-3893

Lifetime (5119 days) 75874 14.82 26.95 18 2-300 2045.13 1116 20-46625 1292.67 387 1-272974

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	4	4.00	32.75	36	23-36	1555.50	1941	399-1941	2973.75	3782.50	437-3893
Last 7 days	18	2.57	30.94	23	7-101	2270.50	1173	399-11874	2158.06	2437	120-3893
Last 30 days	69	2.30	27.94	21	5-190	4719.07	1413	360-29220	1384.23	872	44-3893
Lifetime (5119 days)	75874	14.82	26.95	18	2-300	2045.13	1116	20-46625	1292.67	387	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	64185	84.6
HKY85	5991	7.9
010000	860	1.1
REV	830	1.1
TRN93	558	0.7
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	27558	36.3
10-20	3019	4.0
20-30	2443	3.2
30-40	2272	3.0
40-50	1868	2.5
50-60	1974	2.6
60-70	1449	1.9
70-80	1325	1.7
80-90	1225	1.6
90-100	1087	1.4
> 100	31654	41.7

Number of breakpoints	Times found	% found
0	23199	30.6
1	19188	25.3
2	12040	15.9
3	7012	9.2
4	4270	5.6
5	2934	3.9
6	1898	2.5
7	1417	1.9
8	940	1.2
9	761	1.0
≥ 10	2215	2.9

SBP

SBP usage summary as of Fri Dec 4 00:02:32 2020 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 5 0.71 59.20 35 23-107 12.40 17 1-23 4913.40 311 44-23026

Last 30 days 12 0.40 142.92 104 21-492 16.33 4.50 1-73 2825.58 876 31-23026

Lifetime (2766 days) 21192 7.66 50.18 25 2-656 21.74 1 1-45015 602.88 44 0-683633

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	5	0.71	59.20	35	23-107	12.40	17	1-23	4913.40	311	44-23026
Last 30 days	12	0.40	142.92	104	21-492	16.33	4.50	1-73	2825.58	876	31-23026
Lifetime (2766 days)	21192	7.66	50.18	25	2-656	21.74	1	1-45015	602.88	44	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	15364	72.5
REV	1315	6.2
010000	565	2.7
F81	503	2.4
TRN93	502	2.4
0123455	283	1.3
010232	215	1.0
012012	137	0.6
0112304567	122	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	9173	43.3
10-20	911	4.3
20-30	802	3.8
30-40	656	3.1
40-50	519	2.4
50-60	413	1.9
60-70	361	1.7
70-80	378	1.8
80-90	293	1.4
90-100	328	1.5
> 100	7358	34.7

PARRIS

PARRIS usage summary as of Fri Dec 4 00:02:37 2020 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 1353 1353 1353-1353 199 199 199-199

Last 7 days 6 0.86 13.17 10 5-30 1560.50 1273 251-3958 1158 107.50 3-6349

Last 30 days 10 0.33 17.70 14.50 5-34 1070.90 863 120-3958 723.70 61.50 3-6349

Lifetime (4874 days) 14581 2.99 20.12 15 3-75 489.46 329 7-11903 425.90 136 1-48648

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	1353	1353	1353-1353	199	199	199-199
Last 7 days	6	0.86	13.17	10	5-30	1560.50	1273	251-3958	1158	107.50	3-6349
Last 30 days	10	0.33	17.70	14.50	5-34	1070.90	863	120-3958	723.70	61.50	3-6349
Lifetime (4874 days)	14581	2.99	20.12	15	3-75	489.46	329	7-11903	425.90	136	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8250	56.6
F81	1079	7.4
REV	1010	6.9
TRN93	771	5.3
010000	429	2.9
012012	262	1.8
001101	166	1.1
012212	155	1.1
012032	137	0.9
010230	125	0.9

p-values range	Times found	% found
0-0.1	2665	18.3
0.1-0.2	518	3.6
0.2-0.3	474	3.3
0.3-0.4	371	2.5
0.4-0.5	331	2.3
0.5-0.6	392	2.7
0.6-0.7	373	2.6
0.7-0.8	359	2.5
0.8-0.9	355	2.4
0.9-1	8743	60.0

GA Branch

GABranch usage summary as of Fri Dec 4 00:02:40 2020 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 5 5.00 16.80 16 11-30 1842 1353 1273-3958 36727.60 6933 1345-166697

Last 7 days 7 1.00 13.86 11 5-30 1676.86 1273 1255-3958 26275.29 1580 18-166697

Last 30 days 7 0.23 13.86 11 5-30 1676.86 1273 1255-3958 26275.29 1580 18-166697

Lifetime (4867 days) 11845 2.43 13.74 12 3-30 521.60 333 9-11628 5654.43 1515 1-889396

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	5	5.00	16.80	16	11-30	1842	1353	1273-3958	36727.60	6933	1345-166697
Last 7 days	7	1.00	13.86	11	5-30	1676.86	1273	1255-3958	26275.29	1580	18-166697
Last 30 days	7	0.23	13.86	11	5-30	1676.86	1273	1255-3958	26275.29	1580	18-166697
Lifetime (4867 days)	11845	2.43	13.74	12	3-30	521.60	333	9-11628	5654.43	1515	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8572	72.4
REV	614	5.2
010000	568	4.8
F81	415	3.5
TRN93	285	2.4
012012	131	1.1
001101	107	0.9
012212	64	0.5
010012	63	0.5
000010	60	0.5

the number of dN/dS classes range	Times found	% found
1	99	0.8
2	4312	36.4
3	4010	33.9
4	2226	18.8
5	778	6.6
6	237	2.0
7	118	1.0
8	39	0.3
9	26	0.2

CMS

CMS usage summary as of Fri Dec 4 00:02:42 2020 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 1 0.14 35 35 35-35 2466 2466 2466-2466 3623 3623 3623-3623

Last 30 days 2 0.07 54.50 54.50 35-74 2399 2399 2332-2466 5982.50 5982.50 3623-8342

Lifetime (3958 days) 3279 0.83 33.73 24 3-120 570.22 344 7-11276 21081.69 4045 59-3262277

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	1	0.14	35	35	35-35	2466	2466	2466-2466	3623	3623	3623-3623
Last 30 days	2	0.07	54.50	54.50	35-74	2399	2399	2332-2466	5982.50	5982.50	3623-8342
Lifetime (3958 days)	3279	0.83	33.73	24	3-120	570.22	344	7-11276	21081.69	4045	59-3262277

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
0-10	192	5.9
10-20	151	4.6
20-30	193	5.9
30-40	222	6.8
40-50	246	7.5
50-60	180	5.5
60-70	177	5.4
70-80	129	3.9
80-90	178	5.4
90-100	111	3.4
> 100	1500	45.7

Number of rate classes	Times found	% found
1	0	0.0
2	2060	62.8
3	720	22.0
4	279	8.5
5	118	3.6
6	50	1.5
7	15	0.5
8	2	0.1
9	1	0.0
≥ 10	34	1.0

DEPS

DEPS usage summary as of Fri Dec 4 00:02:44 2020 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 2 0.07 17.50 17.50 15-20 5051.50 5051.50 161-9942 36.50 36.50 34-39

Lifetime (3837 days) 3577 0.93 35.84 32 3-100 733.17 528 9-11100 489.42 146 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	0
Last 30 days	2	0.07	17.50	17.50	15-20	5051.50	5051.50	161-9942	36.50	36.50	34-39
Lifetime (3837 days)	3577	0.93	35.84	32	3-100	733.17	528	9-11100	489.42	146	2-31585

Subtyping

SCUEAL usage summary as of Fri Dec 4 00:02:46 2020 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 7002 7002.00 91.42 4 0-500

Last 7 days 7002 1000.29 91.42 4 0-500

Last 30 days 7002 233.40 91.42 4 0-500

Lifetime (4172 days) 8306 1.99 94.63 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	7002	7002.00	91.42	4	0-500
Last 7 days	7002	1000.29	91.42	4	0-500
Last 30 days	7002	233.40	91.42	4	0-500
Lifetime (4172 days)	8306	1.99	94.63	5	0-500

Top 10 Subtypes (out of 785964 sequences)

Subtypes Times found % found

B 310361 39.5

C 152262 19.4

G 51243 6.5

A1 46357 5.9

Complex 32766 4.2

AE 20758 2.6

D 19688 2.5

CRF14 12892 1.6

F1 12305 1.6

B,C recombinant 9775 1.2

Subtypes	Times found	% found
B	310361	39.5
C	152262	19.4
G	51243	6.5
A1	46357	5.9
Complex	32766	4.2
AE	20758	2.6
D	19688	2.5
CRF14	12892	1.6
F1	12305	1.6
B,C recombinant	9775	1.2

Coevolution

BGM usage summary as of Fri Dec 4 00:02:50 2020 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 0

Last 30 days 0

Lifetime (2766 days) 8881 3.21 65.10 30 0-1033 2.25 0.98 0.01-263 2866.47 92 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	0
Last 7 days	0
Last 30 days	0
Lifetime (2766 days)	8881	3.21	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2020