Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Fri Aug 23 00:00:01 2019 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 (3197 days) 92479 28.93 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 (3197 days)	92479	28.93	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 Aug 23 00:00:13 2019 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 202 6.73 35.86 28 3-467 561.36 448 52-3434 388.47 119.50 8-14772

Lifetime (2297 days) 102041 44.42 44.30 24 3-787 483.96 325 1-11276 154.75 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	0
Last 7 days	0
Last 30 days	202	6.73	35.86	28	3-467	561.36	448	52-3434	388.47	119.50	8-14772
Lifetime (2297 days)	102041	44.42	44.30	24	3-787	483.96	325	1-11276	154.75	45	0-51470

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 46116 45.2
REV 13207 12.9
TRN93 10031 9.8
F81 5253 5.1
010000 3926 3.8
010232 2081 2.0
012012 1569 1.5
012212 1383 1.4
010230 1244 1.2
012032 994 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.1 82493 80.8
0.05 0.9 19.1 15116 14.8
0.2 2.1 29.9 2110 2.1
0.25 3.1 32.5 909 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 Fri Aug 23 00:00:27 2019 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 219 7.30 28.65 28 3-45 470.06 444 52-3434 514.29 342 1-6741

Lifetime (2296 days) 56831 24.75 20.67 16 2-110 484.98 322 1-10798 388.16 111 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	219	7.30	28.65	28	3-45	470.06	444	52-3434	514.29	342	1-6741
Lifetime (2296 days)	56831	24.75	20.67	16	2-110	484.98	322	1-10798	388.16	111	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 30127 53.0
REV 5655 10.0
F81 3363 5.9
TRN93 3330 5.9
010000 2339 4.1
012012 1193 2.1
001101 727 1.3
012212 704 1.2
010232 694 1.2
012032 610 1.1

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.9 51397 90.4
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 31.9 746 1.3
95 2.2 30.8 713 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 Fri Aug 23 00:00:33 2019 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 87 87 87-87 226 226 226-226 4250 4250 4250-4250

Lifetime (3377 days) 1077 0.32 47.56 37 7-150 571.15 350 16-3789 3783.42 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	1	0.03	87	87	87-87	226	226	226-226	4250	4250	4250-4250
Lifetime (3377 days)	1077	0.32	47.56	37	7-150	571.15	350	16-3789	3783.42	1973	31-42841

Model Select.

ModelSelection usage summary as of Fri Aug 23 00:00:35 2019 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 1 0.14 21 21 21-21 566 566 566-566

Last 30 days 202 6.73 44.82 18.50 3-472 655.45 684 25-3787

Lifetime (2297 days) 100424 43.72 43.70 22 3-656 519.66 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	1	0.14	21	21	21-21	566	566	566-566
Last 30 days	202	6.73	44.82	18.50	3-472	655.45	684	25-3787
Lifetime (2297 days)	100424	43.72	43.70	22	3-656	519.66	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24093 24.0
TRN93 12953 12.9
F81 8671 8.6
010232 4312 4.3
012012 3484 3.5
012212 3028 3.0
010230 2443 2.4
012232 2390 2.4
012032 2387 2.4
001101 2094 2.1

Model	Times selected	% selected
HKY85	24093	24.0
TRN93	12953	12.9
F81	8671	8.6
010232	4312	4.3
012012	3484	3.5
012212	3028	3.0
010230	2443	2.4
012232	2390	2.4
012032	2387	2.4
001101	2094	2.1

Protein Model Select.

ModelSelectionP usage summary as of Fri Aug 23 00:00:44 2019 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 2 0.29 3 3 3-3 403 403 403-403

Last 30 days 7 0.23 18.14 5 3-42 225.43 214 65-403

Lifetime (4098 days) 3857 0.94 46.21 25 2-499 651.24 440 3-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	2	0.29	3	3	3-3	403	403	403-403
Last 30 days	7	0.23	18.14	5	3-42	225.43	214	65-403
Lifetime (4098 days)	3857	0.94	46.21	25	2-499	651.24	440	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 562 14.6
JTT (Jones,Taylor,Thornton) 406 10.5
BLOSUM62+F 324 8.4
WAG (Whelan and Goldman)+F 320 8.3
WAG (Whelan and Goldman) 244 6.3
HIV (within host)+F 243 6.3
IAV (Influenza A virus)+F 238 6.2
IAV (Influenza A virus) 225 5.8
BLOSUM62 168 4.4
LG (Le and Gascuel) 161 4.2

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	562	14.6
JTT (Jones,Taylor,Thornton)	406	10.5
BLOSUM62+F	324	8.4
WAG (Whelan and Goldman)+F	320	8.3
WAG (Whelan and Goldman)	244	6.3
HIV (within host)+F	243	6.3
IAV (Influenza A virus)+F	238	6.2
IAV (Influenza A virus)	225	5.8
BLOSUM62	168	4.4
LG (Le and Gascuel)	161	4.2

GARD

GARD usage summary as of Fri Aug 23 00:00:46 2019 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 112 3.73 23.74 20 3-94 2550.48 2428.50 432-10302 2652.71 3615 241-11209

Lifetime (4650 days) 75119 16.15 26.86 18 2-300 2035.65 1116 20-46625 1287.30 382 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	112	3.73	23.74	20	3-94	2550.48	2428.50	432-10302	2652.71	3615	241-11209
Lifetime (4650 days)	75119	16.15	26.86	18	2-300	2035.65	1116	20-46625	1287.30	382	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	63430	84.4
HKY85	5991	8.0
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	27270	36.3
10-20	2991	4.0
20-30	2421	3.2
30-40	2252	3.0
40-50	1849	2.5
50-60	1953	2.6
60-70	1427	1.9
70-80	1316	1.8
80-90	1217	1.6
90-100	1081	1.4
> 100	31342	41.7

Number of breakpoints	Times found	% found
0	22936	30.5
1	19014	25.3
2	11918	15.9
3	6928	9.2
4	4224	5.6
5	2905	3.9
6	1875	2.5
7	1409	1.9
8	934	1.2
9	761	1.0
≥ 10	2215	2.9

SBP

SBP usage summary as of Fri Aug 23 00:00:55 2019 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 24 0.80 165.67 121.50 3-472 4.38 1 1-36 1755.75 969.50 0-7480

Lifetime (2297 days) 20729 9.02 49.76 25 2-656 21.85 1 1-45015 595.57 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	0
Last 30 days	24	0.80	165.67	121.50	3-472	4.38	1	1-36	1755.75	969.50	0-7480
Lifetime (2297 days)	20729	9.02	49.76	25	2-656	21.85	1	1-45015	595.57	42	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	14989	72.3
REV	1315	6.3
010000	565	2.7
F81	503	2.4
TRN93	502	2.4
0123455	236	1.1
010232	215	1.0
012012	137	0.7
0112304567	119	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	8986	43.3
10-20	898	4.3
20-30	788	3.8
30-40	644	3.1
40-50	508	2.5
50-60	406	2.0
60-70	358	1.7
70-80	376	1.8
80-90	282	1.4
90-100	315	1.5
> 100	7168	34.6

PARRIS

PARRIS usage summary as of Fri Aug 23 00:00:59 2019 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 25 0.83 9.96 9 4-37 295.32 208 106-1025 513.96 285 6-2883

Lifetime (4405 days) 14410 3.27 20.12 15 3-75 485.80 329 7-11903 426.83 137 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	25	0.83	9.96	9	4-37	295.32	208	106-1025	513.96	285	6-2883
Lifetime (4405 days)	14410	3.27	20.12	15	3-75	485.80	329	7-11903	426.83	137	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8161	56.6
F81	1068	7.4
REV	1008	7.0
TRN93	757	5.3
010000	429	3.0
012012	255	1.8
001101	166	1.2
012212	155	1.1
012032	128	0.9
010230	125	0.9

p-values range	Times found	% found
0-0.1	2627	18.2
0.1-0.2	513	3.6
0.2-0.3	465	3.2
0.3-0.4	365	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	2.5
0.9-1	8636	59.9

GA Branch

GABranch usage summary as of Fri Aug 23 00:01:01 2019 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 16.25 16.50 12-20 813 821 533-1077 18851.25 18912 2872-34709

Lifetime (4398 days) 11727 2.67 13.73 12 3-30 519.37 331 9-11628 5595.67 1520 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	4	0.13	16.25	16.50	12-20	813	821	533-1077	18851.25	18912	2872-34709
Lifetime (4398 days)	11727	2.67	13.73	12	3-30	519.37	331	9-11628	5595.67	1520	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8454	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	3958	33.8
4	2199	18.8
5	774	6.6
6	234	2.0
7	117	1.0
8	37	0.3
9	24	0.2

CMS

CMS usage summary as of Fri Aug 23 00:01:03 2019 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 35.20 35 32-41 1274.80 1364 1032-1532 67298.40 55296 39096-135131

Lifetime (3489 days) 3194 0.92 33.72 24 3-120 563.78 340 7-11276 20749.73 4046 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	5	0.17	35.20	35	32-41	1274.80	1364	1032-1532	67298.40	55296	39096-135131
Lifetime (3489 days)	3194	0.92	33.72	24	3-120	563.78	340	7-11276	20749.73	4046	59-3262277

Distribution of mBIC improvement

Number of inferred rate classes

mBIC improvement range	Times found	% found
0-10	184	5.8
10-20	146	4.6
20-30	188	5.9
30-40	217	6.8
40-50	243	7.6
50-60	178	5.6
60-70	174	5.4
70-80	128	4.0
80-90	175	5.5
90-100	108	3.4
> 100	1453	45.5

Number of rate classes	Times found	% found
1	0	0.0
2	2011	63.0
3	705	22.1
4	270	8.5
5	108	3.4
6	48	1.5
7	15	0.5
8	2	0.1
9	1	0.0
≥ 10	34	1.1

DEPS

DEPS usage summary as of Fri Aug 23 00:01:04 2019 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 36 1.20 43.14 46 4-76 1078.28 471 65-4527 386.28 337.50 7-1245

Lifetime (3368 days) 3167 0.94 34.31 28 3-100 623.36 481 9-11100 512.37 128 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	36	1.20	43.14	46	4-76	1078.28	471	65-4527	386.28	337.50	7-1245
Lifetime (3368 days)	3167	0.94	34.31	28	3-100	623.36	481	9-11100	512.37	128	2-31585

Subtyping

SCUEAL usage summary as of Fri Aug 23 00:01:05 2019 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 6309 6309.00 82.76 4 0-500

Last 7 days 6309 901.29 82.76 4 0-500

Last 30 days 6309 210.30 82.76 4 0-500

Lifetime (3703 days) 7613 2.06 87.74 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	6309	6309.00	82.76	4	0-500
Last 7 days	6309	901.29	82.76	4	0-500
Last 30 days	6309	210.30	82.76	4	0-500
Lifetime (3703 days)	7613	2.06	87.74	5	0-500

Top 10 Subtypes (out of 667940 sequences)

Subtypes Times found % found

B 260574 39.0

C 115814 17.3

G 46053 6.9

A1 41824 6.3

Complex 28102 4.2

AE 19795 3.0

D 18899 2.8

CRF14 11763 1.8

F1 10599 1.6

B,C recombinant 9116 1.4

Subtypes	Times found	% found
B	260574	39.0
C	115814	17.3
G	46053	6.9
A1	41824	6.3
Complex	28102	4.2
AE	19795	3.0
D	18899	2.8
CRF14	11763	1.8
F1	10599	1.6
B,C recombinant	9116	1.4

Coevolution

BGM usage summary as of Fri Aug 23 00:01:08 2019 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 (2297 days) 8881 3.87 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 (2297 days)	8881	3.87	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2019