Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Tue Mar 21 00:00:02 2023 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 (4503 days) 92479 20.54 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 (4503 days)	92479	20.54	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 Mar 21 00:00:14 2023 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 (3603 days) 104431 28.98 44.59 24 3-787 488.42 325 1-11276 182.27 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	0
Last 7 days	0
Last 30 days	0
Lifetime (3603 days)	104431	28.98	44.59	24	3-787	488.42	325	1-11276	182.27	46	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 47603 45.6
REV 13414 12.8
TRN93 10164 9.7
F81 5467 5.2
010000 3929 3.8
010232 2094 2.0
012012 1584 1.5
012212 1406 1.3
010230 1270 1.2
012032 1005 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 23.9 84473 80.9
0.05 0.9 19.1 15415 14.8
0.2 2.1 29.7 2137 2.0
0.25 3.1 31.9 942 0.9
0.01 0.5 15.1 530 0.5
0.5 6.0 43.1 215 0.2
0.15 2.2 22.9 182 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 Mar 21 00:00:33 2023 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 (3602 days) 58372 16.21 20.71 16 2-110 488.51 323 1-11542 389.04 111 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	0
Last 30 days	0
Lifetime (3602 days)	58372	16.21	20.71	16	2-110	488.51	323	1-11542	389.04	111	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 31083 53.2
REV 5725 9.8
F81 3554 6.1
TRN93 3376 5.8
010000 2345 4.0
012012 1240 2.1
001101 730 1.3
012212 720 1.2
010232 709 1.2
012032 623 1.1

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.8 52765 90.4
100 4.4 22.1 1322 2.3
90 19.2 11.2 901 1.5
20 7.2 36.0 826 1.4
95 2.4 31.6 784 1.3
10 5.8 31.7 750 1.3
40 2.5 24.4 145 0.2
25 7.8 34.7 115 0.2
80 3.0 28.9 111 0.2
30 9.8 20.6 93 0.2

TOGGLE

Toggle usage summary as of Tue Mar 21 00:00:40 2023 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 (4683 days) 1095 0.23 47.56 37 7-150 567.74 350 16-3789 3755.66 1966 27-42841

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 (4683 days)	1095	0.23	47.56	37	7-150	567.74	350	16-3789	3755.66	1966	27-42841

Model Select.

ModelSelection usage summary as of Tue Mar 21 00:00:42 2023 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 0

Lifetime (3603 days) 103015 28.59 43.82 22 3-656 523.50 325 1-11935

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	0
Lifetime (3603 days)	103015	28.59	43.82	22	3-656	523.50	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24737 24.0
TRN93 13124 12.7
F81 9029 8.8
010232 4394 4.3
012012 3621 3.5
012212 3103 3.0
010230 2487 2.4
012032 2461 2.4
012232 2439 2.4
001101 2123 2.1

Model	Times selected	% selected
HKY85	24737	24.0
TRN93	13124	12.7
F81	9029	8.8
010232	4394	4.3
012012	3621	3.5
012212	3103	3.0
010230	2487	2.4
012032	2461	2.4
012232	2439	2.4
001101	2123	2.1

Protein Model Select.

ModelSelectionP usage summary as of Tue Mar 21 00:00:51 2023 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 0

Lifetime (5404 days) 4241 0.78 46.17 26 2-500 1067.06 470 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	0
Lifetime (5404 days)	4241	0.78	46.17	26	2-500	1067.06	470	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 570 13.4
JTT (Jones,Taylor,Thornton) 412 9.7
HIV (within host)+F 412 9.7
BLOSUM62+F 341 8.0
WAG (Whelan and Goldman)+F 341 8.0
IAV (Influenza A virus)+F 337 7.9
WAG (Whelan and Goldman) 245 5.8
IAV (Influenza A virus) 228 5.4
HIV (between hosts)+F 180 4.2
BLOSUM62 170 4.0

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	570	13.4
JTT (Jones,Taylor,Thornton)	412	9.7
HIV (within host)+F	412	9.7
BLOSUM62+F	341	8.0
WAG (Whelan and Goldman)+F	341	8.0
IAV (Influenza A virus)+F	337	7.9
WAG (Whelan and Goldman)	245	5.8
IAV (Influenza A virus)	228	5.4
HIV (between hosts)+F	180	4.2
BLOSUM62	170	4.0

GARD

GARD usage summary as of Tue Mar 21 00:00:53 2023 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 3 0.10 42.67 22 18-88 326 354 216-408 62.33 66 41-80

Lifetime (5956 days) 76465 12.84 26.97 18 2-300 2046.21 1116 20-46625 1291.00 386 1-272974

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	0
Last 30 days	3	0.10	42.67	22	18-88	326	354	216-408	62.33	66	41-80
Lifetime (5956 days)	76465	12.84	26.97	18	2-300	2046.21	1116	20-46625	1291.00	386	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	64776	84.7
HKY85	5991	7.8
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	27890	36.5
10-20	3045	4.0
20-30	2447	3.2
30-40	2279	3.0
40-50	1877	2.5
50-60	1982	2.6
60-70	1459	1.9
70-80	1325	1.7
80-90	1228	1.6
90-100	1091	1.4
> 100	31842	41.6

Number of breakpoints	Times found	% found
0	23470	30.7
1	19358	25.3
2	12111	15.8
3	7046	9.2
4	4289	5.6
5	2949	3.9
6	1904	2.5
7	1419	1.9
8	940	1.2
9	764	1.0
≥ 10	2215	2.9

SBP

SBP usage summary as of Tue Mar 21 00:01:02 2023 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 8 0.27 38.50 41 18-75 1.25 1 1-3 554.88 822.50 9-913

Lifetime (3603 days) 21506 5.97 50.76 25 2-656 21.92 1 1-45015 698.48 45 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	0
Last 30 days	8	0.27	38.50	41	18-75	1.25	1	1-3	554.88	822.50	9-913
Lifetime (3603 days)	21506	5.97	50.76	25	2-656	21.92	1	1-45015	698.48	45	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	15612	72.6
REV	1315	6.1
010000	565	2.6
F81	503	2.3
TRN93	502	2.3
0123455	326	1.5
010232	215	1.0
012012	137	0.6
0112304567	128	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	9283	43.2
10-20	919	4.3
20-30	810	3.8
30-40	658	3.1
40-50	528	2.5
50-60	418	1.9
60-70	364	1.7
70-80	380	1.8
80-90	296	1.4
90-100	329	1.5
> 100	7521	35.0

PARRIS

PARRIS usage summary as of Tue Mar 21 00:01:05 2023 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 (5711 days) 14661 2.57 20.08 15 3-75 491.59 329 7-11903 424.60 136 1-48648

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	0
Last 30 days	0
Lifetime (5711 days)	14661	2.57	20.08	15	3-75	491.59	329	7-11903	424.60	136	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8319	56.7
F81	1080	7.4
REV	1011	6.9
TRN93	777	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	2673	18.2
0.1-0.2	518	3.5
0.2-0.3	478	3.3
0.3-0.4	373	2.5
0.4-0.5	332	2.3
0.5-0.6	393	2.7
0.6-0.7	374	2.6
0.7-0.8	361	2.5
0.8-0.9	355	2.4
0.9-1	8804	60.1

GA Branch

GABranch usage summary as of Tue Mar 21 00:01:08 2023 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 (5704 days) 11905 2.09 13.75 12 3-30 522.34 333 9-11628 5646.93 1516 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	0
Lifetime (5704 days)	11905	2.09	13.75	12	3-30	522.34	333	9-11628	5646.93	1516	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8632	72.5
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	4323	36.3
3	4029	33.8
4	2245	18.9
5	783	6.6
6	239	2.0
7	119	1.0
8	40	0.3
9	28	0.2

CMS

CMS usage summary as of Tue Mar 21 00:01:09 2023 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 (4795 days) 3439 0.72 33.10 24 3-120 574.97 352 7-11276 20640.63 4043 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	0
Lifetime (4795 days)	3439	0.72	33.10	24	3-120	574.97	352	7-11276	20640.63	4043	59-3262277

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
0-10	193	5.6
10-20	152	4.4
20-30	199	5.8
30-40	234	6.8
40-50	256	7.4
50-60	184	5.4
60-70	180	5.2
70-80	133	3.9
80-90	181	5.3
90-100	112	3.3
> 100	1615	47.0

Number of rate classes	Times found	% found
1	0	0.0
2	2122	61.7
3	753	21.9
4	315	9.2
5	139	4.0
6	56	1.6
7	17	0.5
8	2	0.1
9	1	0.0
≥ 10	34	1.0

DEPS

DEPS usage summary as of Tue Mar 21 00:01:11 2023 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 (4674 days) 3766 0.81 35.79 31 3-100 1082.48 556 9-11100 473.30 141 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	0
Lifetime (4674 days)	3766	0.81	35.79	31	3-100	1082.48	556	9-11100	473.30	141	2-31585

Subtyping

SCUEAL usage summary as of Tue Mar 21 00:01:12 2023 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 7376 7376.00 88.40 4 0-500

Last 7 days 7376 1053.71 88.40 4 0-500

Last 30 days 7376 245.87 88.40 4 0-500

Lifetime (5009 days) 8680 1.73 91.92 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	7376	7376.00	88.40	4	0-500
Last 7 days	7376	1053.71	88.40	4	0-500
Last 30 days	7376	245.87	88.40	4	0-500
Lifetime (5009 days)	8680	1.73	91.92	5	0-500

Top 10 Subtypes (out of 797859 sequences)

Subtypes Times found % found

B 314265 39.4

C 153099 19.2

G 52864 6.6

A1 47172 5.9

Complex 33834 4.2

AE 20841 2.6

D 19948 2.5

CRF14 12971 1.6

F1 12729 1.6

B,C recombinant 9957 1.2

Subtypes	Times found	% found
B	314265	39.4
C	153099	19.2
G	52864	6.6
A1	47172	5.9
Complex	33834	4.2
AE	20841	2.6
D	19948	2.5
CRF14	12971	1.6
F1	12729	1.6
B,C recombinant	9957	1.2

Coevolution

BGM usage summary as of Tue Mar 21 00:01:14 2023 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 (3603 days) 8881 2.46 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 (3603 days)	8881	2.46	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2023