Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Tue Jan 28 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 (3355 days) 92479 27.56 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 (3355 days)	92479	27.56	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 Jan 28 00:00:13 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 4.00 189.25 183.50 10-380 381.25 408.50 142-566 2238 1681 892-4698

Last 7 days 58 8.29 114.17 42 6-488 552.48 210 42-3391 2855.57 935 279-22346

Last 30 days 91 3.03 96.62 41 4-488 535.05 297 42-3391 2616.78 1300 248-22346

Lifetime (2455 days) 102527 41.76 44.37 24 3-787 484.22 325 1-11276 159.58 45 0-51470

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	189.25	183.50	10-380	381.25	408.50	142-566	2238	1681	892-4698
Last 7 days	58	8.29	114.17	42	6-488	552.48	210	42-3391	2855.57	935	279-22346
Last 30 days	91	3.03	96.62	41	4-488	535.05	297	42-3391	2616.78	1300	248-22346
Lifetime (2455 days)	102527	41.76	44.37	24	3-787	484.22	325	1-11276	159.58	45	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 46423 45.3
REV 13237 12.9
TRN93 10072 9.8
F81 5271 5.1
010000 3928 3.8
010232 2083 2.0
012012 1581 1.5
012212 1390 1.4
010230 1256 1.2
012032 996 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.1 82923 80.9
0.05 0.9 19.1 15156 14.8
0.2 2.1 29.8 2118 2.1
0.25 3.1 32.4 915 0.9
0.01 0.4 14.7 520 0.5
0.5 5.9 43.2 214 0.2
0.15 2.5 23.5 161 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 Jan 28 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 4 4.00 14.25 13 11-20 430.75 531 89-572 898.50 926 124-1618

Last 7 days 9 1.29 21.33 15 9-49 325.44 392 76-572 669.22 254 124-1618

Last 30 days 21 0.70 23.33 19 5-52 462.62 503 76-1980 600.05 375 101-1618

Lifetime (2454 days) 57125 23.28 20.68 16 2-110 485.09 323 1-10798 389.11 111 0-54132

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	4	4.00	14.25	13	11-20	430.75	531	89-572	898.50	926	124-1618
Last 7 days	9	1.29	21.33	15	9-49	325.44	392	76-572	669.22	254	124-1618
Last 30 days	21	0.70	23.33	19	5-52	462.62	503	76-1980	600.05	375	101-1618
Lifetime (2454 days)	57125	23.28	20.68	16	2-110	485.09	323	1-10798	389.11	111	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 30307 53.1
REV 5678 9.9
F81 3395 5.9
TRN93 3337 5.8
010000 2341 4.1
012012 1204 2.1
001101 728 1.3
012212 704 1.2
010232 694 1.2
012032 614 1.1

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.8 51685 90.5
100 4.3 22.4 1301 2.3
90 19.2 11.2 900 1.6
20 7.2 35.9 820 1.4
10 5.8 31.9 747 1.3
95 2.2 30.9 717 1.3
40 2.5 24.4 145 0.3
80 3.0 28.0 109 0.2
30 10.0 20.2 91 0.2
25 3.4 36.7 86 0.2

TOGGLE

Toggle usage summary as of Tue Jan 28 00:00:33 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 (3535 days) 1081 0.31 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 (3535 days)	1081	0.31	47.60	37	7-150	571.64	350	16-3789	3781.73	1968	31-42841

Model Select.

ModelSelection usage summary as of Tue Jan 28 00:00:35 2020 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 9 9.00 96 20 8-380 457.44 251 85-1983

Last 7 days 45 6.43 173.71 98 6-488 413.93 213 22-3391

Last 30 days 87 2.90 117.17 31 3-488 523.78 515 22-3391

Lifetime (2455 days) 101065 41.17 43.73 22 3-656 520.10 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	9	9.00	96	20	8-380	457.44	251	85-1983
Last 7 days	45	6.43	173.71	98	6-488	413.93	213	22-3391
Last 30 days	87	2.90	117.17	31	3-488	523.78	515	22-3391
Lifetime (2455 days)	101065	41.17	43.73	22	3-656	520.10	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24263 24.0
TRN93 13005 12.9
F81 8710 8.6
010232 4328 4.3
012012 3541 3.5
012212 3049 3.0
010230 2464 2.4
012032 2409 2.4
012232 2404 2.4
001101 2096 2.1

Model	Times selected	% selected
HKY85	24263	24.0
TRN93	13005	12.9
F81	8710	8.6
010232	4328	4.3
012012	3541	3.5
012212	3049	3.0
010230	2464	2.4
012032	2409	2.4
012232	2404	2.4
001101	2096	2.1

Protein Model Select.

ModelSelectionP usage summary as of Tue Jan 28 00:00:44 2020 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 3 0.43 93 93 93-93 566 566 566-566

Last 30 days 9 0.30 69.22 93 16-121 582.78 566 183-947

Lifetime (4256 days) 3889 0.91 46.52 25 2-500 651.81 444 3-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	3	0.43	93	93	93-93	566	566	566-566
Last 30 days	9	0.30	69.22	93	16-121	582.78	566	183-947
Lifetime (4256 days)	3889	0.91	46.52	25	2-500	651.81	444	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 564 14.5
JTT (Jones,Taylor,Thornton) 407 10.5
BLOSUM62+F 326 8.4
WAG (Whelan and Goldman)+F 321 8.3
HIV (within host)+F 254 6.5
WAG (Whelan and Goldman) 244 6.3
IAV (Influenza A virus)+F 241 6.2
IAV (Influenza A virus) 228 5.9
BLOSUM62 169 4.3
LG (Le and Gascuel) 163 4.2

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	564	14.5
JTT (Jones,Taylor,Thornton)	407	10.5
BLOSUM62+F	326	8.4
WAG (Whelan and Goldman)+F	321	8.3
HIV (within host)+F	254	6.5
WAG (Whelan and Goldman)	244	6.3
IAV (Influenza A virus)+F	241	6.2
IAV (Influenza A virus)	228	5.9
BLOSUM62	169	4.3
LG (Le and Gascuel)	163	4.2

GARD

GARD usage summary as of Tue Jan 28 00:00:46 2020 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 0

Last 7 days 7 1.00 50.86 49 11-76 665.14 639 228-1593 674.71 528 379-1483

Last 30 days 14 0.47 59.07 45.50 5-138 1710.64 1630.50 228-5940 1712.79 932.50 379-3805

Lifetime (4808 days) 75365 15.67 26.89 18 2-300 2036.76 1116 20-46625 1289.05 384 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	7	1.00	50.86	49	11-76	665.14	639	228-1593	674.71	528	379-1483
Last 30 days	14	0.47	59.07	45.50	5-138	1710.64	1630.50	228-5940	1712.79	932.50	379-3805
Lifetime (4808 days)	75365	15.67	26.89	18	2-300	2036.76	1116	20-46625	1289.05	384	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	63676	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	27372	36.3
10-20	3000	4.0
20-30	2428	3.2
30-40	2259	3.0
40-50	1854	2.5
50-60	1961	2.6
60-70	1436	1.9
70-80	1317	1.7
80-90	1219	1.6
90-100	1083	1.4
> 100	31436	41.7

Number of breakpoints	Times found	% found
0	23031	30.6
1	19064	25.3
2	11952	15.9
3	6953	9.2
4	4243	5.6
5	2913	3.9
6	1885	2.5
7	1413	1.9
8	935	1.2
9	761	1.0
≥ 10	2215	2.9

SBP

SBP usage summary as of Tue Jan 28 00:00:55 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 15 2.14 71 76 6-267 25.33 6 1-166 465 167 16-2957

Last 30 days 29 0.97 68.66 76 6-267 15.03 1 1-166 568.62 416 16-2957

Lifetime (2455 days) 20886 8.51 49.85 25 2-656 21.77 1 1-45015 597.15 42 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	15	2.14	71	76	6-267	25.33	6	1-166	465	167	16-2957
Last 30 days	29	0.97	68.66	76	6-267	15.03	1	1-166	568.62	416	16-2957
Lifetime (2455 days)	20886	8.51	49.85	25	2-656	21.77	1	1-45015	597.15	42	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	15125	72.4
REV	1315	6.3
010000	565	2.7
F81	503	2.4
TRN93	502	2.4
0123455	248	1.2
010232	215	1.0
012012	137	0.7
0112304567	119	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	9046	43.3
10-20	901	4.3
20-30	799	3.8
30-40	648	3.1
40-50	511	2.4
50-60	410	2.0
60-70	359	1.7
70-80	376	1.8
80-90	285	1.4
90-100	320	1.5
> 100	7231	34.6

PARRIS

PARRIS usage summary as of Tue Jan 28 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 4 0.13 23.50 24 22-24 1179.25 1141 1141-1294 463.25 516 232-589

Lifetime (4563 days) 14462 3.17 20.13 15 3-75 487.21 329 7-11903 426.33 137 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	4	0.13	23.50	24	22-24	1179.25	1141	1141-1294	463.25	516	232-589
Lifetime (4563 days)	14462	3.17	20.13	15	3-75	487.21	329	7-11903	426.33	137	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8175	56.5
F81	1068	7.4
REV	1008	7.0
TRN93	758	5.2
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	2645	18.3
0.1-0.2	514	3.6
0.2-0.3	466	3.2
0.3-0.4	366	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	358	2.5
0.8-0.9	354	2.4
0.9-1	8667	59.9

GA Branch

GABranch usage summary as of Tue Jan 28 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 5 0.17 22.60 25 11-27 674.20 684 343-1029 7263.40 6664 1237-13060

Lifetime (4556 days) 11735 2.58 13.74 12 3-30 520.07 332 9-11628 5664.97 1521 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	5	0.17	22.60	25	11-27	674.20	684	343-1029	7263.40	6664	1237-13060
Lifetime (4556 days)	11735	2.58	13.74	12	3-30	520.07	332	9-11628	5664.97	1521	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8462	72.1
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	4285	36.5
3	3961	33.8
4	2201	18.8
5	774	6.6
6	234	2.0
7	118	1.0
8	38	0.3
9	25	0.2

CMS

CMS usage summary as of Tue Jan 28 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 2 0.29 34.50 34.50 26-43 229 229 229-229 4923 4923 3604-6242

Last 30 days 16 0.53 45.38 25 3-118 683.19 758 229-1029 23670.12 3124 409-123741

Lifetime (3647 days) 3230 0.89 33.79 24 3-120 564.01 341 7-11276 21207.87 4060 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	34.50	34.50	26-43	229	229	229-229	4923	4923	3604-6242
Last 30 days	16	0.53	45.38	25	3-118	683.19	758	229-1029	23670.12	3124	409-123741
Lifetime (3647 days)	3230	0.89	33.79	24	3-120	564.01	341	7-11276	21207.87	4060	59-3262277

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
0-10	185	5.7
10-20	149	4.6
20-30	189	5.9
30-40	217	6.7
40-50	243	7.5
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	1479	45.8

Number of rate classes	Times found	% found
1	0	0.0
2	2030	62.8
3	708	21.9
4	274	8.5
5	116	3.6
6	50	1.5
7	15	0.5
8	2	0.1
9	1	0.0
≥ 10	34	1.1

DEPS

DEPS usage summary as of Tue Jan 28 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 85 85 77-93 566 566 566-566 2223.50 2223.50 673-3774

Last 30 days 7 0.23 45.14 26 20-93 629.71 566 183-947 932.43 585 70-3774

Lifetime (3526 days) 3414 0.97 35.26 30 3-100 653.00 503.50 9-11100 501.78 140 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	85	85	77-93	566	566	566-566	2223.50	2223.50	673-3774
Last 30 days	7	0.23	45.14	26	20-93	629.71	566	183-947	932.43	585	70-3774
Lifetime (3526 days)	3414	0.97	35.26	30	3-100	653.00	503.50	9-11100	501.78	140	2-31585

Subtyping

SCUEAL usage summary as of Tue Jan 28 00:01:05 2020 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 6519 6519.00 83.51 4 0-500

Last 7 days 6519 931.29 83.51 4 0-500

Last 30 days 6519 217.30 83.51 4 0-500

Lifetime (3861 days) 7823 2.03 88.23 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	6519	6519.00	83.51	4	0-500
Last 7 days	6519	931.29	83.51	4	0-500
Last 30 days	6519	217.30	83.51	4	0-500
Lifetime (3861 days)	7823	2.03	88.23	5	0-500

Top 10 Subtypes (out of 690213 sequences)

Subtypes Times found % found

B 261615 37.9

C 134745 19.5

G 46124 6.7

A1 42206 6.1

Complex 28401 4.1

AE 19846 2.9

D 18998 2.8

CRF14 11763 1.7

F1 10630 1.5

B,C recombinant 9225 1.3

Subtypes	Times found	% found
B	261615	37.9
C	134745	19.5
G	46124	6.7
A1	42206	6.1
Complex	28401	4.1
AE	19846	2.9
D	18998	2.8
CRF14	11763	1.7
F1	10630	1.5
B,C recombinant	9225	1.3

Coevolution

BGM usage summary as of Tue Jan 28 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 (2455 days) 8881 3.62 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 (2455 days)	8881	3.62	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2020