Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Tue Jul 14 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 (3523 days) 92479 26.25 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 (3523 days)	92479	26.25	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 Tue Jul 14 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 3 3.00 32 28 28-40 1273.33 1273 1273-1274 3456.67 3091 2331-4948

Last 7 days 15 2.14 57.07 28 5-334 1401.40 1273 183-3304 4514.60 3507 1017-11072

Last 30 days 50 1.67 46.34 22 3-334 782.80 433.50 79-3433 2251.22 1387.50 213-11072

Lifetime (2623 days) 103365 39.41 44.51 24 3-787 486.98 325 1-11276 177.33 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	3	3.00	32	28	28-40	1273.33	1273	1273-1274	3456.67	3091	2331-4948
Last 7 days	15	2.14	57.07	28	5-334	1401.40	1273	183-3304	4514.60	3507	1017-11072
Last 30 days	50	1.67	46.34	22	3-334	782.80	433.50	79-3433	2251.22	1387.50	213-11072
Lifetime (2623 days)	103365	39.41	44.51	24	3-787	486.98	325	1-11276	177.33	46	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 46917 45.4
REV 13299 12.9
TRN93 10127 9.8
F81 5368 5.2
010000 3929 3.8
010232 2092 2.0
012012 1582 1.5
012212 1394 1.3
010230 1268 1.2
012032 1002 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.0 83561 80.8
0.05 0.9 19.1 15309 14.8
0.2 2.1 29.7 2131 2.1
0.25 3.1 31.8 932 0.9
0.01 0.4 14.7 522 0.5
0.5 5.9 43.2 214 0.2
0.15 2.3 21.7 174 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 Tue Jul 14 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 0

Last 7 days 4 0.57 13 11.50 6-23 895 612.50 538-1817 1752.25 988 185-4848

Last 30 days 55 1.83 18.05 11 6-74 512.64 219 76-1951 511.11 178 41-5604

Lifetime (2622 days) 57825 22.05 20.70 16 2-110 487.07 323 1-10798 390.56 111 0-54132

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	4	0.57	13	11.50	6-23	895	612.50	538-1817	1752.25	988	185-4848
Last 30 days	55	1.83	18.05	11	6-74	512.64	219	76-1951	511.11	178	41-5604
Lifetime (2622 days)	57825	22.05	20.70	16	2-110	487.07	323	1-10798	390.56	111	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 30763 53.2
REV 5694 9.8
F81 3507 6.1
TRN93 3354 5.8
010000 2341 4.0
012012 1205 2.1
001101 730 1.3
010232 707 1.2
012212 704 1.2
012032 614 1.1

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.8 52259 90.4
100 4.4 22.1 1318 2.3
90 19.2 11.2 901 1.6
20 7.2 35.8 822 1.4
95 2.4 31.6 764 1.3
10 5.8 31.9 747 1.3
40 2.5 24.4 145 0.3
25 7.8 34.6 114 0.2
80 3.0 28.0 109 0.2
30 10.0 20.2 91 0.2

TOGGLE

Toggle usage summary as of Tue Jul 14 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 1 0.03 22 22 22-22 219 219 219-219 394 394 394-394

Lifetime (3703 days) 1088 0.29 47.56 37 7-150 569.25 350 16-3789 3770.49 1970.50 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	1	0.03	22	22	22-22	219	219	219-219	394	394	394-394
Lifetime (3703 days)	1088	0.29	47.56	37	7-150	569.25	350	16-3789	3770.49	1970.50	31-42841

Model Select.

ModelSelection usage summary as of Tue Jul 14 00:00:35 2020 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 14 2.00 18.57 11 5-105 1306.86 1033.50 183-4405

Last 30 days 101 3.37 33.90 13 5-305 660.32 354 76-9744

Lifetime (2623 days) 101935 38.86 43.83 22 3-656 521.63 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	14	2.00	18.57	11	5-105	1306.86	1033.50	183-4405
Last 30 days	101	3.37	33.90	13	5-305	660.32	354	76-9744
Lifetime (2623 days)	101935	38.86	43.83	22	3-656	521.63	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24474 24.0
TRN93 13078 12.8
F81 8844 8.7
010232 4361 4.3
012012 3561 3.5
012212 3059 3.0
010230 2481 2.4
012032 2419 2.4
012232 2417 2.4
001101 2111 2.1

Model	Times selected	% selected
HKY85	24474	24.0
TRN93	13078	12.8
F81	8844	8.7
010232	4361	4.3
012012	3561	3.5
012212	3059	3.0
010230	2481	2.4
012032	2419	2.4
012232	2417	2.4
001101	2111	2.1

Protein Model Select.

ModelSelectionP usage summary as of Tue Jul 14 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 3 0.10 148.67 15 15-416 169.33 192 124-192

Lifetime (4424 days) 3933 0.89 46.56 25 2-500 670.43 444 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	3	0.10	148.67	15	15-416	169.33	192	124-192
Lifetime (4424 days)	3933	0.89	46.56	25	2-500	670.43	444	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 567 14.4
JTT (Jones,Taylor,Thornton) 409 10.4
BLOSUM62+F 326 8.3
WAG (Whelan and Goldman)+F 323 8.2
HIV (within host)+F 269 6.8
WAG (Whelan and Goldman) 245 6.2
IAV (Influenza A virus)+F 242 6.2
IAV (Influenza A virus) 228 5.8
BLOSUM62 169 4.3
LG (Le and Gascuel) 166 4.2

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	567	14.4
JTT (Jones,Taylor,Thornton)	409	10.4
BLOSUM62+F	326	8.3
WAG (Whelan and Goldman)+F	323	8.2
HIV (within host)+F	269	6.8
WAG (Whelan and Goldman)	245	6.2
IAV (Influenza A virus)+F	242	6.2
IAV (Influenza A virus)	228	5.8
BLOSUM62	169	4.3
LG (Le and Gascuel)	166	4.2

GARD

GARD usage summary as of Tue Jul 14 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 13 12 10-17 2850.50 3100.50 1815-3195 2140 2176.50 330-3833

Last 30 days 39 1.30 18.67 16 5-80 2225.46 2778 192-3303 1634.28 871 182-3928

Lifetime (4976 days) 75657 15.20 26.93 18 2-300 2039.92 1116 20-46625 1290.83 385 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	13	12	10-17	2850.50	3100.50	1815-3195	2140	2176.50	330-3833
Last 30 days	39	1.30	18.67	16	5-80	2225.46	2778	192-3303	1634.28	871	182-3928
Lifetime (4976 days)	75657	15.20	26.93	18	2-300	2039.92	1116	20-46625	1290.83	385	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	63968	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	27507	36.4
10-20	3009	4.0
20-30	2436	3.2
30-40	2266	3.0
40-50	1861	2.5
50-60	1969	2.6
60-70	1444	1.9
70-80	1322	1.7
80-90	1219	1.6
90-100	1084	1.4
> 100	31540	41.7

Number of breakpoints	Times found	% found
0	23150	30.6
1	19131	25.3
2	12002	15.9
3	6972	9.2
4	4258	5.6
5	2922	3.9
6	1892	2.5
7	1416	1.9
8	938	1.2
9	761	1.0
≥ 10	2215	2.9

SBP

SBP usage summary as of Tue Jul 14 00:00:56 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 1.00 202 202 202-202 1 1 1-1 968 968 968-968

Last 7 days 2 0.29 111.50 111.50 21-202 1 1 1-1 946 946 924-968

Last 30 days 18 0.60 76.56 15 6-338 54.50 71 1-161 341.89 8 4-1049

Lifetime (2623 days) 21089 8.04 50.12 25 2-656 21.75 1 1-45015 601.07 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	1	1.00	202	202	202-202	1	1	1-1	968	968	968-968
Last 7 days	2	0.29	111.50	111.50	21-202	1	1	1-1	946	946	924-968
Last 30 days	18	0.60	76.56	15	6-338	54.50	71	1-161	341.89	8	4-1049
Lifetime (2623 days)	21089	8.04	50.12	25	2-656	21.75	1	1-45015	601.07	43	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	15287	72.5
REV	1315	6.2
010000	565	2.7
F81	503	2.4
TRN93	502	2.4
0123455	266	1.3
010232	215	1.0
012012	137	0.6
0112304567	120	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	9137	43.3
10-20	909	4.3
20-30	800	3.8
30-40	654	3.1
40-50	515	2.4
50-60	412	2.0
60-70	360	1.7
70-80	377	1.8
80-90	290	1.4
90-100	321	1.5
> 100	7314	34.7

PARRIS

PARRIS usage summary as of Tue Jul 14 00:00:59 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 30 1.00 12.73 11 10-22 192.70 175 109-400 44.17 24.50 8-187

Lifetime (4731 days) 14552 3.08 20.11 15 3-75 488.81 329 7-11903 425.90 137 1-48648

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	0
Last 30 days	30	1.00	12.73	11	10-22	192.70	175	109-400	44.17	24.50	8-187
Lifetime (4731 days)	14552	3.08	20.11	15	3-75	488.81	329	7-11903	425.90	137	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8226	56.5
F81	1077	7.4
REV	1010	6.9
TRN93	769	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	2663	18.3
0.1-0.2	515	3.5
0.2-0.3	472	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	373	2.6
0.7-0.8	359	2.5
0.8-0.9	355	2.4
0.9-1	8724	60.0

GA Branch

GABranch usage summary as of Tue Jul 14 00:01:01 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 1 0.03 15 15 15-15 123 123 123-123 492 492 492-492

Lifetime (4724 days) 11823 2.50 13.73 12 3-30 520.57 333 9-11628 5643.38 1510 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	0
Last 30 days	1	0.03	15	15	15-15	123	123	123-123	492	492	492-492
Lifetime (4724 days)	11823	2.50	13.73	12	3-30	520.57	333	9-11628	5643.38	1510	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8550	72.3
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	4308	36.4
3	4002	33.8
4	2219	18.8
5	777	6.6
6	236	2.0
7	118	1.0
8	39	0.3
9	25	0.2

CMS

CMS usage summary as of Tue Jul 14 00:01:03 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 72 72 72-72 1005 1005 1005-1005 108737 108737 108737-108737

Last 30 days 8 0.27 33.38 37.50 12-72 425.38 400.50 123-1005 35687.12 23765 952-108737

Lifetime (3815 days) 3266 0.86 33.70 24 3-120 568.38 343 7-11276 21118.97 4031 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	72	72	72-72	1005	1005	1005-1005	108737	108737	108737-108737
Last 30 days	8	0.27	33.38	37.50	12-72	425.38	400.50	123-1005	35687.12	23765	952-108737
Lifetime (3815 days)	3266	0.86	33.70	24	3-120	568.38	343	7-11276	21118.97	4031	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	191	5.8
30-40	222	6.8
40-50	246	7.5
50-60	179	5.5
60-70	176	5.4
70-80	129	3.9
80-90	177	5.4
90-100	111	3.4
> 100	1492	45.7

Number of rate classes	Times found	% found
1	0	0.0
2	2053	62.9
3	716	21.9
4	278	8.5
5	117	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 Tue Jul 14 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 10 1.43 34.20 35 27-38 1274 1274 1274-1274 145.60 138.50 92-209

Last 30 days 114 3.80 45.20 46 15-51 1009.86 1000 192-1274 209.40 192 25-528

Lifetime (3694 days) 3558 0.96 35.76 31.50 3-100 710.70 526 9-11100 489.86 145.50 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	10	1.43	34.20	35	27-38	1274	1274	1274-1274	145.60	138.50	92-209
Last 30 days	114	3.80	45.20	46	15-51	1009.86	1000	192-1274	209.40	192	25-528
Lifetime (3694 days)	3558	0.96	35.76	31.50	3-100	710.70	526	9-11100	489.86	145.50	2-31585

Subtyping

SCUEAL usage summary as of Tue Jul 14 00:01:06 2020 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 6644 6644.00 84.10 4 0-500

Last 7 days 6644 949.14 84.10 4 0-500

Last 30 days 6644 221.47 84.10 4 0-500

Lifetime (4029 days) 7948 1.97 88.65 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	6644	6644.00	84.10	4	0-500
Last 7 days	6644	949.14	84.10	4	0-500
Last 30 days	6644	221.47	84.10	4	0-500
Lifetime (4029 days)	7948	1.97	88.65	5	0-500

Top 10 Subtypes (out of 704602 sequences)

Subtypes Times found % found

B 263343 37.4

C 144342 20.5

G 46814 6.6

A1 42427 6.0

Complex 28830 4.1

AE 19960 2.8

D 19014 2.7

CRF14 11765 1.7

F1 10663 1.5

B,C recombinant 9472 1.3

Subtypes	Times found	% found
B	263343	37.4
C	144342	20.5
G	46814	6.6
A1	42427	6.0
Complex	28830	4.1
AE	19960	2.8
D	19014	2.7
CRF14	11765	1.7
F1	10663	1.5
B,C recombinant	9472	1.3

Coevolution

BGM usage summary as of Tue Jul 14 00:01:08 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 (2623 days) 8881 3.39 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 (2623 days)	8881	3.39	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2020