Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Fri Apr 3 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 (3421 days) 92479 27.03 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 (3421 days)	92479	27.03	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 Apr 3 00:00:14 2020 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 15 15.00 126.47 7 7-483 489.27 419 419-759 256.93 10 9-1163

Last 7 days 63 9.00 88.51 12 3-483 645.83 424 75-3972 1773.10 298 2-18639

Last 30 days 179 5.97 72.30 26 3-483 935.34 446 53-9744 4661.41 2455 2-45868

Lifetime (2521 days) 102880 40.81 44.45 24 3-787 485.32 325 1-11276 173.18 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	15	15.00	126.47	7	7-483	489.27	419	419-759	256.93	10	9-1163
Last 7 days	63	9.00	88.51	12	3-483	645.83	424	75-3972	1773.10	298	2-18639
Last 30 days	179	5.97	72.30	26	3-483	935.34	446	53-9744	4661.41	2455	2-45868
Lifetime (2521 days)	102880	40.81	44.45	24	3-787	485.32	325	1-11276	173.18	46	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 46644 45.3
REV 13270 12.9
TRN93 10088 9.8
F81 5313 5.2
010000 3928 3.8
010232 2083 2.0
012012 1582 1.5
012212 1391 1.4
010230 1265 1.2
012032 998 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.0 83176 80.8
0.05 0.9 19.1 15237 14.8
0.2 2.1 29.8 2122 2.1
0.25 3.1 31.9 928 0.9
0.01 0.4 14.7 520 0.5
0.5 5.9 43.2 214 0.2
0.15 2.5 23.4 162 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 Apr 3 00:00:27 2020 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 18 18.00 7 7 7-7 419 419 419-419 15.28 15 6-29

Last 7 days 69 9.86 6.19 4 3-21 436.48 419 52-1273 90.97 29 0-1257

Last 30 days 167 5.57 19.83 12 3-71 637.20 419 52-9744 884.63 202 0-29079

Lifetime (2520 days) 57417 22.78 20.67 16 2-110 486.68 323 1-10798 391.14 111 0-54132

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	18	18.00	7	7	7-7	419	419	419-419	15.28	15	6-29
Last 7 days	69	9.86	6.19	4	3-21	436.48	419	52-1273	90.97	29	0-1257
Last 30 days	167	5.57	19.83	12	3-71	637.20	419	52-9744	884.63	202	0-29079
Lifetime (2520 days)	57417	22.78	20.67	16	2-110	486.68	323	1-10798	391.14	111	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 30498 53.1
REV 5686 9.9
F81 3457 6.0
TRN93 3344 5.8
010000 2341 4.1
012012 1205 2.1
001101 730 1.3
012212 704 1.2
010232 698 1.2
012032 614 1.1

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.8 51929 90.4
100 4.4 22.2 1312 2.3
90 19.2 11.2 901 1.6
20 7.2 35.9 821 1.4
10 5.8 31.9 747 1.3
95 2.2 31.0 723 1.3
40 2.5 24.4 145 0.3
80 3.0 28.0 109 0.2
25 8.6 34.1 104 0.2
30 10.0 20.2 91 0.2

TOGGLE

Toggle usage summary as of Fri Apr 3 00:00:34 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 (3601 days) 1081 0.30 47.60 37 7-150 571.64 350 16-3789 3781.73 1968 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 (3601 days)	1081	0.30	47.60	37	7-150	571.64	350	16-3789	3781.73	1968	31-42841

Model Select.

ModelSelection usage summary as of Fri Apr 3 00:00:36 2020 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 5 5.00 365.40 462 7-483 629.80 716 419-759

Last 7 days 32 4.57 172.72 36.50 3-483 889.51 514 186.33-3972

Last 30 days 134 4.47 88.07 36 3-483 855.04 296.50 57-9744

Lifetime (2521 days) 101317 40.19 43.81 22 3-656 520.66 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	5	5.00	365.40	462	7-483	629.80	716	419-759
Last 7 days	32	4.57	172.72	36.50	3-483	889.51	514	186.33-3972
Last 30 days	134	4.47	88.07	36	3-483	855.04	296.50	57-9744
Lifetime (2521 days)	101317	40.19	43.81	22	3-656	520.66	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24329 24.0
TRN93 13025 12.9
F81 8750 8.6
010232 4337 4.3
012012 3554 3.5
012212 3050 3.0
010230 2474 2.4
012032 2413 2.4
012232 2408 2.4
001101 2098 2.1

Model	Times selected	% selected
HKY85	24329	24.0
TRN93	13025	12.9
F81	8750	8.6
010232	4337	4.3
012012	3554	3.5
012212	3050	3.0
010230	2474	2.4
012032	2413	2.4
012232	2408	2.4
001101	2098	2.1

Protein Model Select.

ModelSelectionP usage summary as of Fri Apr 3 00:00:45 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 9 0.30 32.44 32 3-52 5658.56 9626 621-9744

Lifetime (4322 days) 3900 0.90 46.49 25 2-500 663.48 445.50 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	9	0.30	32.44	32	3-52	5658.56	9626	621-9744
Lifetime (4322 days)	3900	0.90	46.49	25	2-500	663.48	445.50	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 564 14.5
JTT (Jones,Taylor,Thornton) 407 10.4
BLOSUM62+F 326 8.4
WAG (Whelan and Goldman)+F 323 8.3
HIV (within host)+F 259 6.6
WAG (Whelan and Goldman) 244 6.3
IAV (Influenza A virus)+F 241 6.2
IAV (Influenza A virus) 228 5.8
BLOSUM62 169 4.3
LG (Le and Gascuel) 166 4.3

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	564	14.5
JTT (Jones,Taylor,Thornton)	407	10.4
BLOSUM62+F	326	8.4
WAG (Whelan and Goldman)+F	323	8.3
HIV (within host)+F	259	6.6
WAG (Whelan and Goldman)	244	6.3
IAV (Influenza A virus)+F	241	6.2
IAV (Influenza A virus)	228	5.8
BLOSUM62	169	4.3
LG (Le and Gascuel)	166	4.3

GARD

GARD usage summary as of Fri Apr 3 00:00:47 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 6 0.86 116.17 74.50 12-262 3867 3648 1206-9342 3019.17 4112.50 326-4649

Last 30 days 33 1.10 55 23 4-262 5080.27 1539 171-29103 3012 976 294-29966

Lifetime (4874 days) 75487 15.49 26.92 18 2-300 2039.86 1116 20-46625 1290.43 385 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	6	0.86	116.17	74.50	12-262	3867	3648	1206-9342	3019.17	4112.50	326-4649
Last 30 days	33	1.10	55	23	4-262	5080.27	1539	171-29103	3012	976	294-29966
Lifetime (4874 days)	75487	15.49	26.92	18	2-300	2039.86	1116	20-46625	1290.43	385	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	63798	84.5
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	27437	36.3
10-20	3008	4.0
20-30	2432	3.2
30-40	2260	3.0
40-50	1855	2.5
50-60	1965	2.6
60-70	1439	1.9
70-80	1319	1.7
80-90	1219	1.6
90-100	1084	1.4
> 100	31469	41.7

Number of breakpoints	Times found	% found
0	23092	30.6
1	19098	25.3
2	11963	15.8
3	6960	9.2
4	4247	5.6
5	2916	3.9
6	1886	2.5
7	1414	1.9
8	935	1.2
9	761	1.0
≥ 10	2215	2.9

SBP

SBP usage summary as of Fri Apr 3 00:00:57 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 4 0.57 119.25 31 19-396 3.25 2.50 1-7 1491.75 442.50 161-4921

Last 30 days 32 1.07 64.19 33 11-396 5.03 1 1-78 1951.47 495 34-28626

Lifetime (2521 days) 20961 8.31 49.96 25 2-656 21.77 1 1-45015 601.24 43 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	4	0.57	119.25	31	19-396	3.25	2.50	1-7	1491.75	442.50	161-4921
Last 30 days	32	1.07	64.19	33	11-396	5.03	1	1-78	1951.47	495	34-28626
Lifetime (2521 days)	20961	8.31	49.96	25	2-656	21.77	1	1-45015	601.24	43	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	15189	72.5
REV	1315	6.3
010000	565	2.7
F81	503	2.4
TRN93	502	2.4
0123455	254	1.2
010232	215	1.0
012012	137	0.7
0112304567	120	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	9076	43.3
10-20	903	4.3
20-30	799	3.8
30-40	648	3.1
40-50	512	2.4
50-60	410	2.0
60-70	360	1.7
70-80	376	1.8
80-90	286	1.4
90-100	320	1.5
> 100	7271	34.7

PARRIS

PARRIS usage summary as of Fri Apr 3 00:01:00 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 7 7 7-7 419 419 419-419 20 20 20-20

Last 7 days 5 0.71 5.60 6 4-7 1371.20 514 419-3972 25.80 20 12-56

Last 30 days 10 0.33 11.20 6 4-33 1608.80 576 182-3984 881 63.50 12-4683

Lifetime (4629 days) 14484 3.13 20.12 15 3-75 488.42 329 7-11903 426.46 137 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	7	7	7-7	419	419	419-419	20	20	20-20
Last 7 days	5	0.71	5.60	6	4-7	1371.20	514	419-3972	25.80	20	12-56
Last 30 days	10	0.33	11.20	6	4-33	1608.80	576	182-3984	881	63.50	12-4683
Lifetime (4629 days)	14484	3.13	20.12	15	3-75	488.42	329	7-11903	426.46	137	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8184	56.5
F81	1071	7.4
REV	1008	7.0
TRN93	766	5.3
010000	429	3.0
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	2649	18.3
0.1-0.2	514	3.5
0.2-0.3	467	3.2
0.3-0.4	369	2.5
0.4-0.5	331	2.3
0.5-0.6	391	2.7
0.6-0.7	370	2.6
0.7-0.8	359	2.5
0.8-0.9	354	2.4
0.9-1	8680	59.9

GA Branch

GABranch usage summary as of Fri Apr 3 00:01:02 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 2 0.29 15 15 6-24 2235.50 2235.50 514-3957 71913 71913 536-143290

Last 30 days 4 0.13 11.25 8 5-24 1422.25 656.50 419-3957 36145.25 552.50 186-143290

Lifetime (4622 days) 11762 2.54 13.74 12 3-30 520.44 331 9-11628 5665.76 1516.50 1-889396

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	15	6-24	2235.50	2235.50	514-3957	71913	71913	536-143290
Last 30 days	4	0.13	11.25	8	5-24	1422.25	656.50	419-3957	36145.25	552.50	186-143290
Lifetime (4622 days)	11762	2.54	13.74	12	3-30	520.44	331	9-11628	5665.76	1516.50	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8489	72.2
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	4299	36.5
3	3973	33.8
4	2201	18.7
5	774	6.6
6	234	2.0
7	118	1.0
8	39	0.3
9	25	0.2

CMS

CMS usage summary as of Fri Apr 3 00:01:04 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 2 0.29 49.50 49.50 24-75 2208 2208 459-3957 39425.50 39425.50 4708-74143

Last 30 days 7 0.23 32.57 24 7-75 1319 562 85-3957 19377.43 7210 1960-74143

Lifetime (3713 days) 3250 0.88 33.73 24 3-120 569.02 343 7-11276 21126.57 4044 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	2	0.29	49.50	49.50	24-75	2208	2208	459-3957	39425.50	39425.50	4708-74143
Last 30 days	7	0.23	32.57	24	7-75	1319	562	85-3957	19377.43	7210	1960-74143
Lifetime (3713 days)	3250	0.88	33.73	24	3-120	569.02	343	7-11276	21126.57	4044	59-3262277

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
0-10	190	5.8
10-20	151	4.6
20-30	190	5.8
30-40	221	6.8
40-50	246	7.6
50-60	179	5.5
60-70	174	5.4
70-80	129	4.0
80-90	175	5.4
90-100	111	3.4
> 100	1484	45.7

Number of rate classes	Times found	% found
1	0	0.0
2	2044	62.9
3	712	21.9
4	276	8.5
5	116	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 Apr 3 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 0

Last 7 days 0

Last 30 days 12 0.40 45 52 20-52 8326.33 9647.50 555-9744 242.17 170.50 88-455

Lifetime (3592 days) 3427 0.95 35.29 30 3-100 679.81 508 9-11100 500.74 141 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	12	0.40	45	52	20-52	8326.33	9647.50	555-9744	242.17	170.50	88-455
Lifetime (3592 days)	3427	0.95	35.29	30	3-100	679.81	508	9-11100	500.74	141	2-31585

Subtyping

SCUEAL usage summary as of Fri Apr 3 00:01:07 2020 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 6587 6587.00 83.95 4 0-500

Last 7 days 6587 941.00 83.95 4 0-500

Last 30 days 6587 219.57 83.95 4 0-500

Lifetime (3927 days) 7891 2.01 88.56 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	6587	6587.00	83.95	4	0-500
Last 7 days	6587	941.00	83.95	4	0-500
Last 30 days	6587	219.57	83.95	4	0-500
Lifetime (3927 days)	7891	2.01	88.56	5	0-500

Top 10 Subtypes (out of 698835 sequences)

Subtypes Times found % found

B 263256 37.7

C 140163 20.1

G 46494 6.7

A1 42287 6.1

Complex 28631 4.1

AE 19954 2.9

D 19014 2.7

CRF14 11765 1.7

F1 10659 1.5

B,C recombinant 9244 1.3

Subtypes	Times found	% found
B	263256	37.7
C	140163	20.1
G	46494	6.7
A1	42287	6.1
Complex	28631	4.1
AE	19954	2.9
D	19014	2.7
CRF14	11765	1.7
F1	10659	1.5
B,C recombinant	9244	1.3

Coevolution

BGM usage summary as of Fri Apr 3 00:01:09 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 (2521 days) 8881 3.52 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 (2521 days)	8881	3.52	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2020