Sections:
MCMC Post-hoc Analysis: 48 sequences
directory: /home/biodept/br51/Work
subdirectory: 48-fsa-6
command line: bali-phy 48-fsa.fasta --smodel GTR+DP[4]
directory: /home/biodept/br51/Work
subdirectory: 48-fsa-7
command line: bali-phy 48-fsa.fasta --smodel GTR+DP[4]
directory: /home/biodept/br51/Work
subdirectory: 48-fsa-8
command line: bali-phy 48-fsa.fasta --smodel GTR+DP[4]
directory: /home/biodept/br51/Work
subdirectory: 48-fsa-9
command line: bali-phy 48-fsa.fasta --smodel GTR+DP[4]
Partition | Sequences | Lengths | Substitution Model | Indel Model |
1 |
48-fsa.fasta |
110 - 131RNA nucleotides |
GTR+DP[4] |
RS07 |
burn-in = 7530 samples |
sub-sample = 20 |
P(data|M) = -4083.717 +- 0.596
|
Complete sample: 15345
topologies |
95% Bayesian credible interval: 14578 topologies |
chain # | Iterations (after burnin) |
1 |
67773 samples |
2 |
82377 samples |
3 |
70942 samples |
4 |
85782 samples |
Partition support: Summary |
Partition support graph: SVG |
Partition 1
|
|
|
Diff |
|
Min. %identity |
# Sites |
Constant |
Informative |
Initial |
FASTA |
HTML |
Diff |
|
17.7% |
214 |
6 (2.8%) |
187 (87.4%) |
Best (WPD) |
FASTA |
HTML |
|
AU |
28.5% |
212 |
8 (3.77%) |
157 (74.1%) |
- 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 |
---|
433 | 1672 | 654.992 | 0.010 | 0.026
| 1.005 | 1.017 |
Statistic | Median | 95% BCI | ACT | Ne | burnin | PSRF-CI80% | PSRF-RCF |
prior |
-1038 |
(-1110, -973.9) |
5.035 |
3048 |
163
|
0.9995 | 0.9989
| Trace |
prior_A1 |
-754.9 |
(-820, -700.4) |
2.532 |
6061 |
161
|
1.005 | 1.005
| Trace |
likelihood |
-4041 |
(-4082, -3999) |
3.034 |
5058 |
174
|
1.001 | 1.016
| Trace |
logp |
-5079 |
(-5139, -5025) |
4.465 |
3437 |
143
|
1.004 | 1.01
| Trace |
Heat.beta |
1 |
| | | |
Main.mu1 |
0.1603 |
(0.1135, 0.2327) |
1.316 |
11661 |
220
|
1.001 | 1.002
| Trace |
S1.GTR.ag |
0.2004 |
(0.1541, 0.2518) |
1.509 |
10170 |
101
|
0.9991 | 0.9949
| Trace |
S1.GTR.at |
0.2356 |
(0.1797, 0.2975) |
3.071 |
4998 |
199
|
0.9998 | 1
| Trace |
S1.GTR.ac |
0.06871 |
(0.04213, 0.1008) |
1.276 |
12032 |
139
|
1 | 1.009
| Trace |
S1.GTR.gt |
0.04227 |
(0.0201, 0.0703) |
1.677 |
9151 |
170
|
1 | 0.9962
| Trace |
S1.GTR.gc |
0.08834 |
(0.06095, 0.1226) |
1.999 |
7676 |
162
|
0.9983 | 1.005
| Trace |
S1.GTR.tc |
0.36 |
(0.2973, 0.4285) |
1.714 |
8956 |
167
|
1.001 | 0.9969
| Trace |
S1.F.piA |
0.2114 |
(0.1794, 0.2487) |
1.802 |
8517 |
107
|
1 | 1.009
| Trace |
S1.F.piG |
0.2949 |
(0.253, 0.3379) |
1.993 |
7700 |
163
|
0.9995 | 1.006
| Trace |
S1.F.piU |
0.2134 |
(0.1848, 0.2455) |
2.084 |
7363 |
108
|
1.002 | 1.008
| Trace |
S1.F.piC |
0.2786 |
(0.2453, 0.3147) |
1.245 |
12325 |
101
|
1 | 0.9935
| Trace |
S1.DP.f1[S1] |
0.1994 |
(0.1248, 0.286) |
1.311 |
11711 |
109
|
1.004 | 1.003
| Trace |
S1.DP.f2[S1] |
0.3203 |
(0.1267, 0.4655) |
1.446 |
10611 |
79
|
1.002 | 0.9893
| Trace |
S1.DP.f3[S1] |
0.27 |
(0.1054, 0.4183) |
1.211 |
12678 |
170
|
0.9988 | 1.006
| Trace |
S1.DP.f4[S1] |
0.2178 |
(0.07536, 0.3739) |
2.295 |
6686 |
127
|
1 | 0.998
| Trace |
S1.DP.rates1[S1] |
0.008341 |
(0.002243, 0.02007) |
1.462 |
10494 |
123
|
1.001 | 1.005
| Trace |
S1.DP.rates2[S1] |
0.111 |
(0.07307, 0.1646) |
2.127 |
7214 |
146
|
1.001 | 0.9983
| Trace |
S1.DP.rates3[S1] |
0.2623 |
(0.1927, 0.3526) |
1 |
15348 |
103
|
0.9993 | 0.9919
| Trace |
S1.DP.rates4[S1] |
0.6161 |
(0.5132, 0.698) |
1.212 |
12660 |
114
|
0.999 | 0.9923
| Trace |
I1.RS07.logLambda |
-3.565 |
(-3.889, -3.257) |
2.059 |
7454 |
129
|
1.002 | 0.9993
| Trace |
I1.RS07.meanIndelLength |
1.949 |
(1.632, 2.384) |
2.439 |
6293 |
165
|
0.9999 | 0.9945
| Trace |
|A1| |
201 |
(187, 217) |
9.179 |
1672 |
200 |
0.9474 | 1.016
| Trace |
#indels1 |
101 |
(91, 112) |
2.898 |
5296 |
104 |
0.8727 | 1.008
| Trace |
|indels1| |
189 |
(166, 217) |
4.965 |
3091 |
433 |
0.9771 | 1.013
| Trace |
#substs1 |
1023 |
(1002, 1047) |
6.03 |
2545 |
206 |
0.9667 | 1.017
| Trace |
|A| |
201 |
(187, 217) |
9.179 |
1672 |
200 |
0.9474 | 1.016
| Trace |
#indels |
101 |
(91, 112) |
2.898 |
5296 |
104 |
0.8727 | 1.008
| Trace |
|indels| |
189 |
(166, 217) |
4.965 |
3091 |
433 |
0.9771 | 1.013
| Trace |
#substs |
1023 |
(1002, 1047) |
6.03 |
2545 |
206 |
0.9667 | 1.017
| Trace |
|T| |
14.64 |
(11.97, 18.34) |
2.234 |
6868 |
163
|
0.997 | 0.9929
| Trace |