Sections:
MCMC Post-hoc Analysis: 28 sequences
directory: /home/biodept/br51/Work
subdirectory: few-globins-1
command line: bali-phy few-globins.fasta --smodel=LG+DP[6]
directory: /home/biodept/br51/Work
subdirectory: few-globins-2
command line: bali-phy few-globins.fasta --smodel=LG+DP[6]
directory: /home/biodept/br51/Work
subdirectory: few-globins-3
command line: bali-phy few-globins.fasta --smodel=LG+DP[6]
directory: /home/biodept/br51/Work
subdirectory: few-globins-4
command line: bali-phy few-globins.fasta --smodel=LG+DP[6]
Partition | Sequences | Lengths | Substitution Model | Indel Model |
1 |
few-globins.fasta |
141 - 190Amino-Acids |
LG+DP[6] |
RS07 |
burn-in = 2446 samples |
sub-sample = 5 |
P(data|M) = -9470.622 +- 0.675
|
Complete sample: 7311
topologies |
95% Bayesian credible interval: 6109 topologies |
chain # | Iterations (after burnin) |
1 |
34815 samples |
2 |
22021 samples |
3 |
34482 samples |
4 |
37196 samples |
Partition support: Summary |
Partition support graph: SVG |
Partition 1
|
|
|
Diff |
|
Min. %identity |
# Sites |
Constant |
Informative |
Initial |
FASTA |
HTML |
Diff |
|
1.26% |
190 |
0 (0%) |
190 (100%) |
Best (WPD) |
FASTA |
HTML |
|
AU |
8.04% |
353 |
2 (0.567%) |
229 (64.9%) |
- Partition uncertainty
- SRQ plot: partitions
- SRQ plot: c50
- Variation in split frequency estimates
burnin (scalar) | Ne (scalar) | Ne (partition) | ASDSF | MSDSF | PSRF-CI80% | PSRF-RCF |
---|
2192 | 77.71 | 1249.629 | 0.011 | 0.045
| 1.007 | 1.019 |
Statistic | Median | 95% BCI | ACT | Ne | burnin | PSRF-CI80% | PSRF-RCF |
prior |
-877.8 |
(-938.5, -829.3) |
84.25 |
305 |
634
|
0.9964 | 1.007
| Trace |
prior_A1 |
-688.9 |
(-746.1, -646.4) |
102.8 |
250 |
1386
|
0.994 | 0.9972
| Trace |
likelihood |
-9437 |
(-9468, -9404) |
16.6 |
1548 |
319
|
0.9968 | 0.9992
| Trace |
logp |
-1.032e+04 |
(-1.037e+04, -1.027e+04) |
43.69 |
588 |
607
|
1 | 1.008
| Trace |
Heat.beta |
1 |
| | | |
Main.mu1 |
0.4924 |
(0.3387, 0.739) |
1 |
25706 |
202
|
0.9989 | 0.9979
| Trace |
S1.F.piA |
0.1177 |
(0.1052, 0.1306) |
6.934 |
3707 |
235
|
1 | 1.008
| Trace |
S1.F.piR |
0.02769 |
(0.02196, 0.03436) |
7.849 |
3275 |
405
|
1.001 | 0.9816
| Trace |
S1.F.piN |
0.03791 |
(0.03136, 0.04532) |
6.595 |
3897 |
367
|
1.003 | 1.017
| Trace |
S1.F.piD |
0.05681 |
(0.04802, 0.06685) |
7.825 |
3285 |
464
|
1 | 0.9791
| Trace |
S1.F.piC |
0.0139 |
(0.008979, 0.02026) |
6.709 |
3831 |
311
|
0.9995 | 1.01
| Trace |
S1.F.piQ |
0.0333 |
(0.02747, 0.0397) |
7.354 |
3495 |
508
|
1.005 | 0.9932
| Trace |
S1.F.piE |
0.05969 |
(0.05095, 0.06902) |
7.943 |
3236 |
420
|
1.003 | 1.012
| Trace |
S1.F.piG |
0.08591 |
(0.07328, 0.09974) |
7.211 |
3564 |
497
|
0.9998 | 1.007
| Trace |
S1.F.piH |
0.02676 |
(0.02134, 0.03328) |
6.938 |
3705 |
271
|
0.9976 | 0.9969
| Trace |
S1.F.piI |
0.03891 |
(0.03221, 0.04679) |
6.844 |
3755 |
292
|
0.9997 | 1.005
| Trace |
S1.F.piL |
0.08793 |
(0.07487, 0.1023) |
7.878 |
3263 |
389
|
1.002 | 0.9993
| Trace |
S1.F.piK |
0.07105 |
(0.06071, 0.08226) |
9.399 |
2734 |
269
|
1.002 | 1.013
| Trace |
S1.F.piM |
0.02338 |
(0.01832, 0.0293) |
7.327 |
3508 |
245
|
1.001 | 1.006
| Trace |
S1.F.piF |
0.0412 |
(0.03265, 0.05043) |
7.901 |
3253 |
238
|
0.9946 | 0.9765
| Trace |
S1.F.piP |
0.03838 |
(0.03041, 0.0469) |
7.555 |
3402 |
295
|
1 | 0.9853
| Trace |
S1.F.piS |
0.07202 |
(0.06291, 0.08201) |
8.179 |
3142 |
202
|
0.9967 | 1.011
| Trace |
S1.F.piT |
0.05416 |
(0.04586, 0.06291) |
7.226 |
3557 |
357
|
1.002 | 0.9925
| Trace |
S1.F.piW |
0.01064 |
(0.006285, 0.0165) |
7.408 |
3470 |
769
|
1.002 | 1.005
| Trace |
S1.F.piY |
0.02399 |
(0.01801, 0.0311) |
8.453 |
3041 |
169
|
1.007 | 1.019
| Trace |
S1.F.piV |
0.07618 |
(0.06597, 0.08711) |
6.807 |
3776 |
608
|
0.9898 | 0.9752
| Trace |
S1.DP.f1[S1] |
0.06767 |
(0.02522, 0.1484) |
1.537 |
16722 |
227
|
0.9988 | 0.9942
| Trace |
S1.DP.f2[S1] |
0.1579 |
(0.0511, 0.334) |
1.037 |
24790 |
96
|
1.001 | 0.9963
| Trace |
S1.DP.f3[S1] |
0.1805 |
(0.05724, 0.3581) |
1.041 |
24703 |
98
|
0.9986 | 0.9916
| Trace |
S1.DP.f4[S1] |
0.178 |
(0.05826, 0.3578) |
1 |
25706 |
102
|
0.9986 | 0.9988
| Trace |
S1.DP.f5[S1] |
0.1799 |
(0.0593, 0.3558) |
1.023 |
25116 |
138
|
0.9988 | 0.992
| Trace |
S1.DP.f6[S1] |
0.1924 |
(0.06145, 0.3682) |
1 |
25706 |
84
|
0.998 | 0.9979
| Trace |
S1.DP.rates1[S1] |
0.03091 |
(0.008202, 0.05641) |
1.796 |
14314 |
183
|
0.9995 | 0.9973
| Trace |
S1.DP.rates2[S1] |
0.09949 |
(0.06482, 0.1295) |
1.312 |
19590 |
133
|
1.003 | 1.009
| Trace |
S1.DP.rates3[S1] |
0.1373 |
(0.1075, 0.1709) |
1.02 |
25205 |
195
|
0.9975 | 0.9988
| Trace |
S1.DP.rates4[S1] |
0.1766 |
(0.142, 0.2233) |
1.048 |
24524 |
89
|
1.002 | 1.001
| Trace |
S1.DP.rates5[S1] |
0.2361 |
(0.1876, 0.2885) |
1.095 |
23482 |
123
|
0.9985 | 0.9867
| Trace |
S1.DP.rates6[S1] |
0.3152 |
(0.2607, 0.3844) |
1.223 |
21016 |
63
|
1.001 | 1.002
| Trace |
I1.RS07.logLambda |
-4.476 |
(-4.745, -4.222) |
1.776 |
14471 |
135
|
1.002 | 1.01
| Trace |
I1.RS07.meanIndelLength |
3.859 |
(3.159, 4.832) |
1.924 |
13361 |
168
|
1.006 | 1.007
| Trace |
|A1| |
345 |
(319, 365) |
330.8 |
77 |
2192 |
0.9558 | 1.015
| Trace |
#indels1 |
84 |
(78, 93) |
88.36 |
290 |
466 |
0.9 | 0.9929
| Trace |
|indels1| |
301 |
(276, 337) |
5.754 |
4467 |
320 |
0.95 | 1.004
| Trace |
#substs1 |
2045 |
(2023, 2066) |
83.88 |
306 |
726 |
0.9558 | 1.008
| Trace |
|A| |
345 |
(319, 365) |
330.8 |
77 |
2192 |
0.9558 | 1.015
| Trace |
#indels |
84 |
(78, 93) |
88.36 |
290 |
466 |
0.9 | 0.9929
| Trace |
|indels| |
301 |
(276, 337) |
5.754 |
4467 |
320 |
0.95 | 1.004
| Trace |
#substs |
2045 |
(2023, 2066) |
83.88 |
306 |
726 |
0.9558 | 1.008
| Trace |
|T| |
25.43 |
(23.03, 28.33) |
1.689 |
15216 |
193
|
0.9999 | 1.005
| Trace |