Datamonkey.org usage statistics

SLAC

SLAC usage summary as of Fri Oct 10 00:00:01 2008 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 14 14.00 41.21 42 3-68 491.50 189 60-1746 71.76 53.65 2.06- 181.85

Last 7 days 81 11.57 34.78 27 3-135 681.54 373 60-3391 56.55 20.03 1.45- 378.13

Last 30 days 328 10.93 32.26 25 3-150 521.44 253 39-3392 57.41 18.40 1.45- 1660.37

Lifetime (1729 days) 19727 11.41 30.99 19 3-247 366.63 235 2-9794 39.91 15.93 0.99-4721

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	14	14.00	41.21	42	3-68	491.50	189	60-1746	71.76	53.65	2.06- 181.85
Last 7 days	81	11.57	34.78	27	3-135	681.54	373	60-3391	56.55	20.03	1.45- 378.13
Last 30 days	328	10.93	32.26	25	3-150	521.44	253	39-3392	57.41	18.40	1.45- 1660.37
Lifetime (1729 days)	19727	11.41	30.99	19	3-247	366.63	235	2-9794	39.91	15.93	0.99-4721

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 10470 53.1
010000 2443 12.4
REV 2377 12.0
TRN93 618 3.1
F81 578 2.9
012212 318 1.6
001101 176 0.9
012012 167 0.8
010232 146 0.7
012232 125 0.6

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 0.9 12.8 16067 81.4
0.05 0.9 8.5 2850 14.4
0.25 1.4 32.8 240 1.2
0.2 1.2 27.7 169 0.9
0.5 5.2 26.4 110 0.6
0.3 1.2 24.6 84 0.4
0.01 0.5 8.0 53 0.3
0.9 24.9 50.4 31 0.2
0.15 2.1 23.4 26 0.1
50 11.6 31.2 8 0.0

FEL

FEL usage summary as of Fri Oct 10 00:00:16 2008 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 25 25.00 34.16 39 3-89 391.96 186 60-1746 184.24 74 3-1216

Last 7 days 86 12.29 23.19 13 3-89 384.60 401 60-1746 80.30 25 1-1216

Last 30 days 273 9.10 26.55 24 3-100 431.21 267 38-3048 152.14 42 1-2586

Lifetime (1380 days) 10260 7.43 26.05 20 3-110 362.93 248 9-7358 173.16 55 0-10979

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	25	25.00	34.16	39	3-89	391.96	186	60-1746	184.24	74	3-1216
Last 7 days	86	12.29	23.19	13	3-89	384.60	401	60-1746	80.30	25	1-1216
Last 30 days	273	9.10	26.55	24	3-100	431.21	267	38-3048	152.14	42	1-2586
Lifetime (1380 days)	10260	7.43	26.05	20	3-110	362.93	248	9-7358	173.16	55	0-10979

Top 10

Models used Test results by p-value

Model Times Used % Used

HKY85 4257 41.5
REV 1522 14.8
010000 1159 11.3
F81 422 4.1
TRN93 374 3.6
012212 218 2.1
000010 183 1.8
001101 166 1.6
012012 132 1.3
010232 127 1.2

p-value Selected/100 codons Times Used % Used

Positive Negative

0.1 1.0 20.8 8608 83.9
0.05 0.8 13.9 1200 11.7
0.25 2.7 36.8 174 1.7
0.2 1.6 27.0 107 1.0
0.15 1.5 15.4 37 0.4
0.5 5.3 31.7 33 0.3
0.01 0.7 19.0 29 0.3
0.19 0.2 4.5 14 0.1
0.95 33.8 25.7 8 0.1
0.005 0.3 10.5 7 0.1

REL

REL usage summary as of Fri Oct 10 00:00:23 2008 PST.

Timeframe Analyses Sequences Sites CPU time

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

Last 1 days 3 3.00 22.33 24 3-40 100 60 60-180 422.67 333 36-899

Last 7 days 29 4.14 14.76 12 3-40 319.38 284 60-756 399.45 335 2-1209

Last 30 days 140 4.67 18.14 16 3-40 434.14 256 32-3048 494.04 307 2-3386

Lifetime (1380 days) 5845 4.24 15.56 14 2-110 370.28 238 4-7085 582.79 292 0-37794

Timeframe	Analyses	Sequences	Sites	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	3	3.00	22.33	24	3-40	100	60	60-180	422.67	333	36-899
Last 7 days	29	4.14	14.76	12	3-40	319.38	284	60-756	399.45	335	2-1209
Last 30 days	140	4.67	18.14	16	3-40	434.14	256	32-3048	494.04	307	2-3386
Lifetime (1380 days)	5845	4.24	15.56	14	2-110	370.28	238	4-7085	582.79	292	0-37794

Top 10

Models used Test results by Bayes Factor

Model Times Used % Used

HKY85 2714 46.4
010000 933 16.0
REV 417 7.1
TRN93 233 4.0
F81 219 3.7
012212 96 1.6
001101 90 1.5
012012 87 1.5
000010 78 1.3
010232 58 1.0

Bayes Factor Selected/100 codons Times Used % Used

Positive Negative

50 3.2 20.5 4980 85.2
10 6.1 35.0 314 5.4
100 4.8 23.2 181 3.1
20 16.1 17.1 155 2.7
95 3.2 20.4 83 1.4
0.1 65.8 93.0 35 0.6
90 5.2 6.7 27 0.5
40 1.5 20.1 18 0.3
30 0.4 39.8 15 0.3
5 9.2 27.9 7 0.1

Model Selection

ModelSelection usage summary as of Fri Oct 10 00:00:44 2008 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 8 8.00 33.12 37.50 13-48 659.96 344 120-1746

Last 7 days 48 6.86 27.71 18 3-100 948.06 344.17 60-3391

Last 30 days 226 7.53 29.22 21.50 3-150 595.73 234 16-3392

Lifetime (437 days) 4125 9.44 28.75 17 3-150 386.14 230 4-10000

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	8	8.00	33.12	37.50	13-48	659.96	344	120-1746
Last 7 days	48	6.86	27.71	18	3-100	948.06	344.17	60-3391
Last 30 days	226	7.53	29.22	21.50	3-150	595.73	234	16-3392
Lifetime (437 days)	4125	9.44	28.75	17	3-150	386.14	230	4-10000

Top 10 Models

Model Times selected % selected

HKY85 1292 31.3
F81 341 8.3
TRN93 271 6.6
012212 205 5.0
000010 131 3.2
001101 118 2.9
010232 113 2.7
012232 101 2.4
012012 93 2.3
012032 75 1.8

Model	Times selected	% selected
HKY85	1292	31.3
F81	341	8.3
TRN93	271	6.6
012212	205	5.0
000010	131	3.2
001101	118	2.9
010232	113	2.7
012232	101	2.4
012012	93	2.3
012032	75	1.8

Protein Model Selection

ModelSelectionP usage summary as of Fri Oct 10 00:00:46 2008 PST.

Timeframe Analyses Sequences Sites

Total Per 24 hrs Mean Median Range Mean Median Range

Last 1 days 0

Last 7 days 8 1.14 11.75 13 6-16 387.50 393 275-457

Last 30 days 45 1.50 18.87 12 6-84 684.27 477 35-1891

Lifetime (129 days) 83 0.64 29.76 19 5-136 580 440 35-3331

Timeframe	Analyses	Sequences	Sites
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range
Last 1 days	0
Last 7 days	8	1.14	11.75	13	6-16	387.50	393	275-457
Last 30 days	45	1.50	18.87	12	6-84	684.27	477	35-1891
Lifetime (129 days)	83	0.64	29.76	19	5-136	580	440	35-3331

Top 10 Models

Model Times selected % selected

WAG (Whelan and Goldman) 20 24.1
LG (Le and Gascuel) 17 20.5
HIV (between hosts) 16 19.3
JTT (Jones,Taylor,Thornton) 16 19.3
BLOSUM62 6 7.2
HIV (within host) 3 3.6
mtMAM (mammalian mitochondrial) 1 1.2
IAV (Influenza A virus) 1 1.2
Dayhoff 1 1.2
rtREV (reverse transcriptase) 1 1.2

Model	Times selected	% selected
WAG (Whelan and Goldman)	20	24.1
LG (Le and Gascuel)	17	20.5
HIV (between hosts)	16	19.3
JTT (Jones,Taylor,Thornton)	16	19.3
BLOSUM62	6	7.2
HIV (within host)	3	3.6
mtMAM (mammalian mitochondrial)	1	1.2
IAV (Influenza A virus)	1	1.2
Dayhoff	1	1.2
rtREV (reverse transcriptase)	1	1.2

PARRIS

PARRIS usage summary as of Fri Oct 10 00:00:47 2008 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 20 19.50 3-38 118 108.50 60-195 226 242 7-413

Last 7 days 15 2.14 15.47 17 3-38 255.20 217 60-756 247.07 197 7-866

Last 30 days 61 2.03 17.84 18 3-38 517.79 196 40-3048 462.61 222 6-2772

Lifetime (436 days) 1012 2.32 17.28 16.50 3-40 396.51 246 11-4733 538.73 304 3-6779

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	20	19.50	3-38	118	108.50	60-195	226	242	7-413
Last 7 days	15	2.14	15.47	17	3-38	255.20	217	60-756	247.07	197	7-866
Last 30 days	61	2.03	17.84	18	3-38	517.79	196	40-3048	462.61	222	6-2772
Lifetime (436 days)	1012	2.32	17.28	16.50	3-40	396.51	246	11-4733	538.73	304	3-6779

Top 10 models used

Distribution of p-values

Model	Times Used	% Used
HKY85	511	50.5
010000	83	8.2
TRN93	53	5.2
REV	51	5.0
F81	45	4.4
012212	40	4.0
012012	23	2.3
012232	13	1.3
012032	12	1.2
000010	12	1.2

p-values range	Times found	% found
0-0.1	218	21.5
0.1-0.2	38	3.8
0.2-0.3	31	3.1
0.3-0.4	28	2.8
0.4-0.5	35	3.5
0.5-0.6	21	2.1
0.6-0.7	21	2.1
0.7-0.8	36	3.6
0.8-0.9	27	2.7
0.9-1	557	55.0

GA Branch

GABranch usage summary as of Fri Oct 10 00:00:48 2008 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 24 24 24-24 60 60 60-60 1733 1733 1733-1733

Last 7 days 9 1.29 14.33 12 5-27 692.33 373 60-3391 4012.11 1733 98-13423

Last 30 days 85 2.83 12.98 10 4-30 671.65 234 32-3575 8480.09 950 3-253122

Lifetime (429 days) 1127 2.63 14.57 14 3-30 509.98 253 14-10000 7272.29 2529 3-253122

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	24	24	24-24	60	60	60-60	1733	1733	1733-1733
Last 7 days	9	1.29	14.33	12	5-27	692.33	373	60-3391	4012.11	1733	98-13423
Last 30 days	85	2.83	12.98	10	4-30	671.65	234	32-3575	8480.09	950	3-253122
Lifetime (429 days)	1127	2.63	14.57	14	3-30	509.98	253	14-10000	7272.29	2529	3-253122

Top 10 models used

Distribution of the number of dN/dS classes

Model	Times Used	% Used
HKY85	560	49.7
REV	107	9.5
010000	93	8.3
F81	49	4.3
TRN93	39	3.5
012012	31	2.8
000010	25	2.2
012032	20	1.8
011020	16	1.4
012232	14	1.2

the number of dN/dS classes range	Times found	% found
1	1	0.1
2	392	34.8
3	427	37.9
4	202	17.9
5	64	5.7
6	29	2.6
7	10	0.9
8	2	0.2
9	0	0.0

Co-evolution

BGM usage summary as of Fri Oct 10 00:00:49 2008 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 9 9.00 14.89 11 9-29 0.67 0.56 0.45- 1.28 33.56 1 1-240

Last 7 days 15 2.14 19.73 16 7-38 1.57 0.79 0.45- 8.18 1478.13 14 1-19018

Last 30 days 85 2.83 31.69 20 6-244 2.12 1.28 0.07- 21.11 1547.78 131 0-30040

Lifetime (210 days) 711 3.39 57.85 35 3-298 1.80 0.90 0.02- 39.67 989.45 226 0-30040

Timeframe	Analyses	Sites	Interacting pairs/site	CPU time
	Total	Per 24 hrs	Mean	Median	Range	Mean	Median	Range	Mean	Median	Range
Last 1 days	9	9.00	14.89	11	9-29	0.67	0.56	0.45- 1.28	33.56	1	1-240
Last 7 days	15	2.14	19.73	16	7-38	1.57	0.79	0.45- 8.18	1478.13	14	1-19018
Last 30 days	85	2.83	31.69	20	6-244	2.12	1.28	0.07- 21.11	1547.78	131	0-30040
Lifetime (210 days)	711	3.39	57.85	35	3-298	1.80	0.90	0.02- 39.67	989.45	226	0-30040

Sergei L. Kosakovsky Pond, Art Poon and Simon D.W. Frost, 2004-2008