Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Wed Sep 30 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 (3601 days) 92479 25.68 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 (3601 days)	92479	25.68	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 Wed Sep 30 00:00:23 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 19 19 19-19 286 286 286-286 865 865 865-865

Last 7 days 9 1.29 29 25 3-110 672.22 556 236-1274 2851 2748 865-5999

Last 30 days 93 3.10 21.28 11 3-252 424.92 275 38-2201 1667.77 1205 120-8204

Lifetime (2701 days) 103568 38.34 44.51 24 3-787 486.99 325 1-11276 180.41 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	1	1.00	19	19	19-19	286	286	286-286	865	865	865-865
Last 7 days	9	1.29	29	25	3-110	672.22	556	236-1274	2851	2748	865-5999
Last 30 days	93	3.10	21.28	11	3-252	424.92	275	38-2201	1667.77	1205	120-8204
Lifetime (2701 days)	103568	38.34	44.51	24	3-787	486.99	325	1-11276	180.41	46	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 47063 45.4
REV 13313 12.9
TRN93 10130 9.8
F81 5391 5.2
010000 3929 3.8
010232 2092 2.0
012012 1582 1.5
012212 1394 1.3
010230 1269 1.2
012032 1004 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.0 83732 80.8
0.05 0.9 19.1 15327 14.8
0.2 2.1 29.7 2136 2.1
0.25 3.1 31.8 937 0.9
0.01 0.4 14.7 523 0.5
0.5 5.9 43.2 214 0.2
0.15 2.3 21.9 177 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 Wed Sep 30 00:00:37 2020 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 5 5.00 16 19 4-19 240 286 56-286 172.60 165 163-186

Last 7 days 8 1.14 16.12 19 4-31 380.62 286 56-1273 155.12 165 57-264

Last 30 days 32 1.07 17.91 12.50 4-56 735.19 286 56-11542 276.62 165 43-2074

Lifetime (2700 days) 57918 21.45 20.70 16 2-110 487.21 322 1-11542 390.45 111 0-54132

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	5	5.00	16	19	4-19	240	286	56-286	172.60	165	163-186
Last 7 days	8	1.14	16.12	19	4-31	380.62	286	56-1273	155.12	165	57-264
Last 30 days	32	1.07	17.91	12.50	4-56	735.19	286	56-11542	276.62	165	43-2074
Lifetime (2700 days)	57918	21.45	20.70	16	2-110	487.21	322	1-11542	390.45	111	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 30824 53.2
REV 5697 9.8
F81 3514 6.1
TRN93 3354 5.8
010000 2344 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 52350 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 34.7 115 0.2
80 3.0 28.0 109 0.2
30 10.0 20.2 91 0.2

TOGGLE

Toggle usage summary as of Wed Sep 30 00:00:44 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 0

Lifetime (3781 days) 1089 0.29 47.57 37 7-150 569.09 350 16-3789 3770.96 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	0
Last 30 days	0
Lifetime (3781 days)	1089	0.29	47.57	37	7-150	569.09	350	16-3789	3770.96	1973	31-42841

Model Select.

ModelSelection usage summary as of Wed Sep 30 00:00:45 2020 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 2 2.00 11.50 11.50 4-19 171 171 56-286

Last 7 days 60 8.57 18.93 15 3-110 545.37 299.33 56- 3878.67

Last 30 days 102 3.40 20.49 15 3-242 699.34 351.33 56-11542

Lifetime (2701 days) 102146 37.82 43.82 22 3-656 522.20 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	2	2.00	11.50	11.50	4-19	171	171	56-286
Last 7 days	60	8.57	18.93	15	3-110	545.37	299.33	56- 3878.67
Last 30 days	102	3.40	20.49	15	3-242	699.34	351.33	56-11542
Lifetime (2701 days)	102146	37.82	43.82	22	3-656	522.20	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24525 24.0
TRN93 13093 12.8
F81 8870 8.7
010232 4379 4.3
012012 3566 3.5
012212 3069 3.0
010230 2483 2.4
012032 2421 2.4
012232 2420 2.4
001101 2111 2.1

Model	Times selected	% selected
HKY85	24525	24.0
TRN93	13093	12.8
F81	8870	8.7
010232	4379	4.3
012012	3566	3.5
012212	3069	3.0
010230	2483	2.4
012032	2421	2.4
012232	2420	2.4
001101	2111	2.1

Protein Model Select.

ModelSelectionP usage summary as of Wed Sep 30 00:00:55 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 30 30 30-30 269 269 269-269

Lifetime (4502 days) 3937 0.87 46.54 25 2-500 672.57 444 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	30	30	30-30	269	269	269-269
Lifetime (4502 days)	3937	0.87	46.54	25	2-500	672.57	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 324 8.2
HIV (within host)+F 271 6.9
WAG (Whelan and Goldman) 245 6.2
IAV (Influenza A virus)+F 242 6.1
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	324	8.2
HIV (within host)+F	271	6.9
WAG (Whelan and Goldman)	245	6.2
IAV (Influenza A virus)+F	242	6.1
IAV (Influenza A virus)	228	5.8
BLOSUM62	169	4.3
LG (Le and Gascuel)	166	4.2

GARD

GARD usage summary as of Wed Sep 30 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 5 5.00 20.40 24 8-24 3186 4791 171-4791 2880 3681 280-3701

Last 7 days 19 2.71 22.95 23 4-61 3546.63 1698 168-11636 2281.47 3046 280-3800

Last 30 days 32 1.07 18.12 22 3-61 5238.25 3781.50 168-34626 2420.59 3621.50 280-4591

Lifetime (5054 days) 75740 14.99 26.94 18 2-300 2042.90 1116 20-46625 1291.85 386 1-272974

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	20.40	24	8-24	3186	4791	171-4791	2880	3681	280-3701
Last 7 days	19	2.71	22.95	23	4-61	3546.63	1698	168-11636	2281.47	3046	280-3800
Last 30 days	32	1.07	18.12	22	3-61	5238.25	3781.50	168-34626	2420.59	3621.50	280-4591
Lifetime (5054 days)	75740	14.99	26.94	18	2-300	2042.90	1116	20-46625	1291.85	386	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	64051	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	27523	36.3
10-20	3009	4.0
20-30	2438	3.2
30-40	2267	3.0
40-50	1868	2.5
50-60	1973	2.6
60-70	1449	1.9
70-80	1323	1.7
80-90	1220	1.6
90-100	1085	1.4
> 100	31585	41.7

Number of breakpoints	Times found	% found
0	23165	30.6
1	19155	25.3
2	12016	15.9
3	6990	9.2
4	4258	5.6
5	2926	3.9
6	1897	2.5
7	1417	1.9
8	940	1.2
9	761	1.0
≥ 10	2215	2.9

SBP

SBP usage summary as of Wed Sep 30 00:01:06 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 25 3.57 28 15 14-165 1.96 1 1-9 300.56 342 64-610

Last 30 days 35 1.17 24.66 15 3-165 7.23 1 1-144 340.03 308 8-1424

Lifetime (2701 days) 21149 7.83 50.11 25 2-656 21.71 1 1-45015 601.39 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	25	3.57	28	15	14-165	1.96	1	1-9	300.56	342	64-610
Last 30 days	35	1.17	24.66	15	3-165	7.23	1	1-144	340.03	308	8-1424
Lifetime (2701 days)	21149	7.83	50.11	25	2-656	21.71	1	1-45015	601.39	44	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	15337	72.5
REV	1315	6.2
010000	565	2.7
F81	503	2.4
TRN93	502	2.4
0123455	273	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	9153	43.3
10-20	909	4.3
20-30	801	3.8
30-40	656	3.1
40-50	519	2.5
50-60	413	2.0
60-70	361	1.7
70-80	378	1.8
80-90	293	1.4
90-100	327	1.5
> 100	7339	34.7

PARRIS

PARRIS usage summary as of Wed Sep 30 00:01:10 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 39 39 39-39 874 874 874-874 95 95 95-95

Last 30 days 12 0.40 27.67 27.50 21-39 589.75 462 286-1384 61.08 53.50 20-135

Lifetime (4809 days) 14568 3.03 20.11 15 3-75 489.00 329 7-11903 425.51 136.50 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	1	0.14	39	39	39-39	874	874	874-874	95	95	95-95
Last 30 days	12	0.40	27.67	27.50	21-39	589.75	462	286-1384	61.08	53.50	20-135
Lifetime (4809 days)	14568	3.03	20.11	15	3-75	489.00	329	7-11903	425.51	136.50	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8241	56.6
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	2664	18.3
0.1-0.2	517	3.5
0.2-0.3	474	3.3
0.3-0.4	370	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	8733	59.9

GA Branch

GABranch usage summary as of Wed Sep 30 00:01:12 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 26 26 26-26 236 236 236-236 2327 2327 2327-2327

Last 30 days 11 0.37 26.45 26 26-27 847.82 434 236-1384 3628.18 3135 1951-7054

Lifetime (4802 days) 11836 2.46 13.74 12 3-30 520.97 333 9-11628 5642.96 1514 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	1	0.14	26	26	26-26	236	236	236-236	2327	2327	2327-2327
Last 30 days	11	0.37	26.45	26	26-27	847.82	434	236-1384	3628.18	3135	1951-7054
Lifetime (4802 days)	11836	2.46	13.74	12	3-30	520.97	333	9-11628	5642.96	1514	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8563	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	4008	33.9
4	2224	18.8
5	778	6.6
6	237	2.0
7	118	1.0
8	39	0.3
9	25	0.2

CMS

CMS usage summary as of Wed Sep 30 00:01:14 2020 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 0

Last 7 days 0

Last 30 days 2 0.07 21.50 21.50 18-25 413.50 413.50 267-560 4364 4364 1027-7701

Lifetime (3893 days) 3272 0.84 33.71 24 3-120 568.32 344 7-11276 21103.92 4037.50 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	0
Last 30 days	2	0.07	21.50	21.50	18-25	413.50	413.50	267-560	4364	4364	1027-7701
Lifetime (3893 days)	3272	0.84	33.71	24	3-120	568.32	344	7-11276	21103.92	4037.50	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	180	5.5
60-70	177	5.4
70-80	129	3.9
80-90	177	5.4
90-100	111	3.4
> 100	1496	45.7

Number of rate classes	Times found	% found
1	0	0.0
2	2055	62.8
3	718	21.9
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 Wed Sep 30 00:01:15 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 30 30 30-30 269 269 269-269 69 69 69-69

Lifetime (3772 days) 3570 0.95 35.84 32 3-100 730.43 528.50 9-11100 488.88 145.50 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	0
Last 30 days	1	0.03	30	30	30-30	269	269	269-269	69	69	69-69
Lifetime (3772 days)	3570	0.95	35.84	32	3-100	730.43	528.50	9-11100	488.88	145.50	2-31585

Subtyping

SCUEAL usage summary as of Wed Sep 30 00:01:17 2020 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 6971 6971.00 91.35 4 0-500

Last 7 days 6971 995.86 91.35 4 0-500

Last 30 days 6971 232.37 91.35 4 0-500

Lifetime (4107 days) 8275 2.01 94.57 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	6971	6971.00	91.35	4	0-500
Last 7 days	6971	995.86	91.35	4	0-500
Last 30 days	6971	232.37	91.35	4	0-500
Lifetime (4107 days)	8275	2.01	94.57	5	0-500

Top 10 Subtypes (out of 782606 sequences)

Subtypes Times found % found

B 310178 39.6

C 151094 19.3

G 51076 6.5

A1 45978 5.9

Complex 32127 4.1

AE 20674 2.6

D 19648 2.5

CRF14 12892 1.6

F1 12297 1.6

B,C recombinant 9649 1.2

Subtypes	Times found	% found
B	310178	39.6
C	151094	19.3
G	51076	6.5
A1	45978	5.9
Complex	32127	4.1
AE	20674	2.6
D	19648	2.5
CRF14	12892	1.6
F1	12297	1.6
B,C recombinant	9649	1.2

Coevolution

BGM usage summary as of Wed Sep 30 00:01:19 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 (2701 days) 8881 3.29 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 (2701 days)	8881	3.29	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2020