Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Mon Jun 17 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 (3130 days) 92479 29.55 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 (3130 days)	92479	29.55	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 Mon Jun 17 00:00:12 2019 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 11 11.00 33.27 40 21-40 498.91 504 262-566 124.27 85 69-304

Last 7 days 82 11.71 52.51 23 3-446 326.83 312 52-716 614.30 277.50 17-7483

Last 30 days 222 7.40 59.57 23 3-500 555.73 344.50 52-4787 1685.16 494.50 12-39106

Lifetime (2230 days) 101654 45.58 44.27 24 3-787 483.35 325 1-11276 152.41 45 0-39106

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	11	11.00	33.27	40	21-40	498.91	504	262-566	124.27	85	69-304
Last 7 days	82	11.71	52.51	23	3-446	326.83	312	52-716	614.30	277.50	17-7483
Last 30 days	222	7.40	59.57	23	3-500	555.73	344.50	52-4787	1685.16	494.50	12-39106
Lifetime (2230 days)	101654	45.58	44.27	24	3-787	483.35	325	1-11276	152.41	45	0-39106

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 45828 45.1
REV 13201 13.0
TRN93 10018 9.9
F81 5234 5.1
010000 3926 3.9
010232 2081 2.0
012012 1563 1.5
012212 1379 1.4
010230 1241 1.2
012032 991 1.0

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.1 24.1 82241 80.9
0.05 0.9 19.2 15024 14.8
0.2 2.1 30.0 2069 2.0
0.25 3.1 32.5 909 0.9
0.01 0.4 14.7 520 0.5
0.5 5.9 42.7 212 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 Mon Jun 17 00:00:25 2019 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 9 9.00 24.67 23 18-40 365.56 262 53-845 811.44 620 84-1545

Last 7 days 64 9.14 22.75 23 5-57 270.12 227 53-845 1183.42 1125 53-4219

Last 30 days 111 3.70 22.57 23 4-57 399.71 273 53-2103 1655.92 1072 45-19637

Lifetime (2229 days) 56473 25.34 20.64 16 2-110 485.43 322 1-10798 385.52 110 0-54132

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	9	9.00	24.67	23	18-40	365.56	262	53-845	811.44	620	84-1545
Last 7 days	64	9.14	22.75	23	5-57	270.12	227	53-845	1183.42	1125	53-4219
Last 30 days	111	3.70	22.57	23	4-57	399.71	273	53-2103	1655.92	1072	45-19637
Lifetime (2229 days)	56473	25.34	20.64	16	2-110	485.43	322	1-10798	385.52	110	0-54132

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 29865 52.9
REV 5652 10.0
F81 3324 5.9
TRN93 3324 5.9
010000 2336 4.1
012012 1185 2.1
001101 727 1.3
012212 702 1.2
010232 694 1.2
012032 608 1.1

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 4.3 27.8 51049 90.4
100 4.2 22.4 1300 2.3
90 19.2 11.2 900 1.6
20 7.2 36.0 819 1.5
10 5.8 31.9 746 1.3
95 2.2 30.8 707 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 Mon Jun 17 00:00:31 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 28 28 28-28 3434 3434 3434-3434 3965 3965 3965-3965

Lifetime (3310 days) 1076 0.33 47.52 37 7-150 571.47 350 16-3789 3782.98 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	28	28	28-28	3434	3434	3434-3434	3965	3965	3965-3965
Lifetime (3310 days)	1076	0.33	47.52	37	7-150	571.47	350	16-3789	3782.98	1970.50	31-42841

Model Select.

ModelSelection usage summary as of Mon Jun 17 00:00:32 2019 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 15 15.00 262.47 428 21-478 551 566 469-845

Last 7 days 172 24.57 211.09 187.50 3-499 424.49 495 21-845

Last 30 days 391 13.03 169.16 120 3-500 505.31 469 21-3434

Lifetime (2230 days) 99963 44.83 43.55 22 3-656 518.48 325 1-11935

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	15	15.00	262.47	428	21-478	551	566	469-845
Last 7 days	172	24.57	211.09	187.50	3-499	424.49	495	21-845
Last 30 days	391	13.03	169.16	120	3-500	505.31	469	21-3434
Lifetime (2230 days)	99963	44.83	43.55	22	3-656	518.48	325	1-11935

Top 10 Models

Model Times selected % selected

HKY85 24034 24.0
TRN93 12924 12.9
F81 8634 8.6
010232 4305 4.3
012012 3440 3.4
012212 3011 3.0
010230 2419 2.4
012232 2379 2.4
012032 2363 2.4
001101 2085 2.1

Model	Times selected	% selected
HKY85	24034	24.0
TRN93	12924	12.9
F81	8634	8.6
010232	4305	4.3
012012	3440	3.4
012212	3011	3.0
010230	2419	2.4
012232	2379	2.4
012032	2363	2.4
001101	2085	2.1

Protein Model Select.

ModelSelectionP usage summary as of Mon Jun 17 00:00:40 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 22 22 22-22 225 225 225-225

Last 30 days 6 0.20 150.17 125 22-299 1707.67 1351 225-3557

Lifetime (4031 days) 3843 0.95 46.26 25 2-499 652.61 444 3-18120

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	1	0.14	22	22	22-22	225	225	225-225
Last 30 days	6	0.20	150.17	125	22-299	1707.67	1351	225-3557
Lifetime (4031 days)	3843	0.95	46.26	25	2-499	652.61	444	3-18120

Top 10 Models

Model Times selected % selected

JTT (Jones,Taylor,Thornton)+F 560 14.6
JTT (Jones,Taylor,Thornton) 404 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) 223 5.8
BLOSUM62 167 4.3
LG (Le and Gascuel) 161 4.2

Model	Times selected	% selected
JTT (Jones,Taylor,Thornton)+F	560	14.6
JTT (Jones,Taylor,Thornton)	404	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)	223	5.8
BLOSUM62	167	4.3
LG (Le and Gascuel)	161	4.2

GARD

GARD usage summary as of Mon Jun 17 00:00:42 2019 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 35.25 40 21-40 1558.50 1512 1512-1698 881.25 441 408-2235

Last 7 days 26 3.71 31.85 24 3-86 1062.69 1247 83-2130 1878.96 1024.50 408-6097

Last 30 days 98 3.27 33.53 23.50 3-161 2320.10 1324.50 83-14361 2623.14 2439 222-11590

Lifetime (4583 days) 74929 16.35 26.86 18 2-300 2034.15 1113 20-46625 1283.43 380 1-272974

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	35.25	40	21-40	1558.50	1512	1512-1698	881.25	441	408-2235
Last 7 days	26	3.71	31.85	24	3-86	1062.69	1247	83-2130	1878.96	1024.50	408-6097
Last 30 days	98	3.27	33.53	23.50	3-161	2320.10	1324.50	83-14361	2623.14	2439	222-11590
Lifetime (4583 days)	74929	16.35	26.86	18	2-300	2034.15	1113	20-46625	1283.43	380	1-272974

Top 10 models used

Distribution of delta AIC

Number of inferred breakpoints

Model	Times Used	% Used
0	63240	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	27223	36.3
10-20	2989	4.0
20-30	2415	3.2
30-40	2243	3.0
40-50	1848	2.5
50-60	1952	2.6
60-70	1422	1.9
70-80	1314	1.8
80-90	1216	1.6
90-100	1077	1.4
> 100	31230	41.7

Number of breakpoints	Times found	% found
0	22892	30.6
1	18979	25.3
2	11895	15.9
3	6894	9.2
4	4194	5.6
5	2889	3.9
6	1869	2.5
7	1407	1.9
8	934	1.2
9	761	1.0
≥ 10	2215	3.0

SBP

SBP usage summary as of Mon Jun 17 00:00:51 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 15 2.14 48.67 69 3-88 23.87 1 1-135 287 184 1-1314

Last 30 days 56 1.87 76.80 38 3-437 13.71 1 1-264 3786.29 219 1-74373

Lifetime (2230 days) 20673 9.27 49.57 25 2-656 21.78 1 1-45015 578.44 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	48.67	69	3-88	23.87	1	1-135	287	184	1-1314
Last 30 days	56	1.87	76.80	38	3-437	13.71	1	1-264	3786.29	219	1-74373
Lifetime (2230 days)	20673	9.27	49.57	25	2-656	21.78	1	1-45015	578.44	42	0-683633

Top 10 models used

Distribution of IC improvement

Model	Times Used	% Used
HKY85	14941	72.3
REV	1315	6.4
010000	565	2.7
F81	503	2.4
TRN93	502	2.4
0123455	232	1.1
010232	215	1.0
012012	137	0.7
0112304567	117	0.6
010230	105	0.5

IC improvement range	Times found	% found
0-10	8952	43.3
10-20	897	4.3
20-30	788	3.8
30-40	640	3.1
40-50	508	2.5
50-60	406	2.0
60-70	353	1.7
70-80	375	1.8
80-90	282	1.4
90-100	315	1.5
> 100	7157	34.6

PARRIS

PARRIS usage summary as of Mon Jun 17 00:00:54 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 13 0.43 19.77 18 4-47 551.77 225 107-1575 2187.15 1799 41-4863

Lifetime (4338 days) 14362 3.31 20.15 15 3-75 486.52 329 7-11903 426.65 137 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	13	0.43	19.77	18	4-47	551.77	225	107-1575	2187.15	1799	41-4863
Lifetime (4338 days)	14362	3.31	20.15	15	3-75	486.52	329	7-11903	426.65	137	1-48648

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	8130	56.6
F81	1064	7.4
REV	1005	7.0
TRN93	756	5.3
010000	429	3.0
012012	252	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	2623	18.3
0.1-0.2	510	3.6
0.2-0.3	463	3.2
0.3-0.4	365	2.5
0.4-0.5	330	2.3
0.5-0.6	390	2.7
0.6-0.7	368	2.6
0.7-0.8	357	2.5
0.8-0.9	352	2.5
0.9-1	8604	59.9

GA Branch

GABranch usage summary as of Mon Jun 17 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 3 0.10 14.33 13 12-18 411 429 363-441 27771 24069 6313-52931

Lifetime (4331 days) 11714 2.70 13.73 12 3-30 519.20 331 9-11628 5573.69 1520.50 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	3	0.10	14.33	13	12-18	411	429	363-441	27771	24069	6313-52931
Lifetime (4331 days)	11714	2.70	13.73	12	3-30	519.20	331	9-11628	5573.69	1520.50	1-889396

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	8441	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	4277	36.5
3	3957	33.8
4	2199	18.8
5	773	6.6
6	233	2.0
7	116	1.0
8	36	0.3
9	24	0.2

CMS

CMS usage summary as of Mon Jun 17 00:00:56 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 2 0.29 54.50 54.50 26-83 221 221 132-310 43238 43238 28743-57733

Last 30 days 4 0.13 41.50 28.50 26-83 1066.25 349.50 132-3434 31984.25 28462 13280-57733

Lifetime (3422 days) 3184 0.93 33.68 24 3-120 556.76 340 7-11276 18863.52 4029.50 59-2971964

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	54.50	54.50	26-83	221	221	132-310	43238	43238	28743-57733
Last 30 days	4	0.13	41.50	28.50	26-83	1066.25	349.50	132-3434	31984.25	28462	13280-57733
Lifetime (3422 days)	3184	0.93	33.68	24	3-120	556.76	340	7-11276	18863.52	4029.50	59-2971964

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	216	6.8
40-50	243	7.6
50-60	178	5.6
60-70	174	5.5
70-80	128	4.0
80-90	175	5.5
90-100	108	3.4
> 100	1444	45.4

Number of rate classes	Times found	% found
1	0	0.0
2	2009	63.1
3	704	22.1
4	266	8.4
5	107	3.4
6	48	1.5
7	14	0.4
8	2	0.1
9	0	0.0
≥ 10	34	1.1

DEPS

DEPS usage summary as of Mon Jun 17 00:00:57 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 1 0.14 11 11 11-11 52 52 52-52 102 102 102-102

Last 30 days 4 0.13 41.50 37 11-81 1105 405.50 52-3557 1394.75 1383 102-2711

Lifetime (3301 days) 3129 0.95 34.18 27 3-100 618.29 481 9-11100 513.08 126 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	1	0.14	11	11	11-11	52	52	52-52	102	102	102-102
Last 30 days	4	0.13	41.50	37	11-81	1105	405.50	52-3557	1394.75	1383	102-2711
Lifetime (3301 days)	3129	0.95	34.18	27	3-100	618.29	481	9-11100	513.08	126	2-31585

Subtyping

SCUEAL usage summary as of Mon Jun 17 00:00:58 2019 PST.

Timeframe Analyses Sequences
Total Per 24 hrs Mean Median Range

Last 1 days 6201 6201.00 83.28 4 0-500

Last 7 days 6201 885.86 83.28 4 0-500

Last 30 days 6201 206.70 83.28 4 0-500

Lifetime (3636 days) 7505 2.06 88.24 5 0-500

Timeframe	Analyses	Sequences
	Total	Per 24 hrs	Mean	Median	Range
Last 1 days	6201	6201.00	83.28	4	0-500
Last 7 days	6201	885.86	83.28	4	0-500
Last 30 days	6201	206.70	83.28	4	0-500
Lifetime (3636 days)	7505	2.06	88.24	5	0-500

Top 10 Subtypes (out of 662226 sequences)

Subtypes Times found % found

B 258992 39.1

C 113210 17.1

G 46009 6.9

A1 41601 6.3

Complex 27852 4.2

AE 19756 3.0

D 18841 2.8

CRF14 11763 1.8

F1 10530 1.6

B,C recombinant 8931 1.3

Subtypes	Times found	% found
B	258992	39.1
C	113210	17.1
G	46009	6.9
A1	41601	6.3
Complex	27852	4.2
AE	19756	3.0
D	18841	2.8
CRF14	11763	1.8
F1	10530	1.6
B,C recombinant	8931	1.3

Coevolution

BGM usage summary as of Mon Jun 17 00:01:00 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 (2230 days) 8881 3.98 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 (2230 days)	8881	3.98	65.10	30	0-1033	2.25	0.98	0.01-263	2866.47	92	0-2900666

UCSD Viral Evolution Group 2004-2019