Sections: [Data+Model] [Analysis] [Alignment] [Phylogeny] [Mixing] [Parameters]

MCMC Post-hoc Analysis: 25 sequences

directory: /home/biodept/br51/Work
subdirectory: 25-6
command line: bali-phy 25.fasta --smodel GTR+DP[4]

directory: /home/biodept/br51/Work
subdirectory: 25-7
command line: bali-phy 25.fasta --smodel GTR+DP[4]

directory: /home/biodept/br51/Work
subdirectory: 25-8
command line: bali-phy 25.fasta --smodel GTR+DP[4]

directory: /home/biodept/br51/Work
subdirectory: 25-9
command line: bali-phy 25.fasta --smodel GTR+DP[4]

Data & Model

PartitionSequencesLengthsSubstitution ModelIndel Model
1 25.fasta 111 - 131RNA nucleotides GTR+DP[4] RS07

Analysis

burn-in = 10000 samples sub-sample = 10 P(data|M) = -2725.989 +- 0.446
Complete sample: 35951 topologies 95% Bayesian credible interval: 34151 topologies
chain #Iterations (after burnin)
1 90000 samples
2 90000 samples
3 90000 samples
4 90000 samples

Phylogeny Distribution

Partition support: Summary
Partition support graph: SVG
50% consensus+LPDFSVG
66% consensus+LPDFSVG
80% consensus+LPDFSVG
90% consensus+LPDFSVG
95% consensus+LPDFSVG
99% consensus+LPDFSVG
100% consensus+LPDFSVG
MAP+LPDFSVG
greedy+LPDFSVG

Alignment Distribution

Partition 1

Diff Min. %identity # Sites Constant Informative
Initial FASTA HTML Diff 12.7% 131 0 (0%) 126 (96.2%)
Best (WPD) FASTA HTML AU 31.2% 198 11 (5.56%) 124 (62.6%)
SRQ plot for support of each partition.SRQ plot for supprt of 50% consensus tree.

Mixing

  1. Partition uncertainty
  2. SRQ plot: partitions
  3. SRQ plot: c50
  4. Variation in split frequency estimates
burnin (scalar)Ne (scalar)Ne (partition)ASDSFMSDSFPSRF-CI80%PSRF-RCF
920425.7877.6540.0120.038 1.0011.005

Scalar variables

StatisticMedian95% BCIACTNeburninPSRF-CI80%PSRF-RCF
prior -567.5 (-627.9, -517.6) 11.46 3140 338 1.0011.002 Trace
prior_A1 -431.2 (-486.9, -388.8) 8.606 4183 158 0.99971.005 Trace
likelihood -2696 (-2725, -2666) 10.65 3381 182 1.0011 Trace
logp -3263 (-3314, -3220) 9.763 3687 158 1.0011.005 Trace
Heat.beta 1
Main.mu1 0.2622 (0.1645, 0.4394) 1.464 24600 122 10.9978 Trace
S1.GTR.ag 0.1601 (0.1113, 0.2214) 1.442 24971 152 0.99991.001 Trace
S1.GTR.at 0.2911 (0.2102, 0.3807) 1.387 25963 143 0.99980.9997 Trace
S1.GTR.ac 0.02198 (0, 0.06543) 2.498 14414 184 1.0010.9991 Trace
S1.GTR.gt 0.07066 (0.03299, 0.1172) 3.162 11386 128 0.99991.005 Trace
S1.GTR.gc 0.08016 (0.04423, 0.1269) 2.867 12556 193 0.99970.9996 Trace
S1.GTR.tc 0.3677 (0.2872, 0.4551) 1.961 18360 79 10.9975 Trace
S1.F.piA 0.2149 (0.1773, 0.2596) 1.674 21512 129 1.0011.001 Trace
S1.F.piG 0.3056 (0.2602, 0.3539) 1.385 25997 135 10.9997 Trace
S1.F.piU 0.1938 (0.1656, 0.2264) 2.777 12967 239 0.99990.9939 Trace
S1.F.piC 0.2836 (0.2445, 0.3265) 1.975 18232 114 1.0010.9974 Trace
S1.DP.f1[S1] 0.174 (0.1, 0.2706) 1.256 28655 190 10.996 Trace
S1.DP.f2[S1] 0.2992 (0.1048, 0.4885) 1.059 34003 68 1.0011 Trace
S1.DP.f3[S1] 0.2915 (0.09519, 0.4738) 2.042 17633 122 1.0011.005 Trace
S1.DP.f4[S1] 0.2315 (0.09811, 0.3996) 2.87 12543 92 0.99960.9982 Trace
S1.DP.rates1[S1] 0.007786 (0.001219, 0.02499) 1.429 25192 244 0.99990.9996 Trace
S1.DP.rates2[S1] 0.1067 (0.05853, 0.1708) 3.132 11494 213 0.99920.9946 Trace
S1.DP.rates3[S1] 0.2295 (0.1642, 0.3693) 2.215 16251 105 10.9947 Trace
S1.DP.rates4[S1] 0.6489 (0.4967, 0.7554) 3.677 9790 156 0.99760.991 Trace
I1.RS07.logLambda -3.919 (-4.289, -3.551) 2.037 17672 141 1.0011 Trace
I1.RS07.meanIndelLength 2.162 (1.714, 2.893) 17.96 2005 341 10.9961 Trace
|A1| 174 (161, 199) 84.59 425 920 0.92310.9873 Trace
#indels1 58 (50, 67) 6.318 5698 130 0.90911.005 Trace
|indels1| 121 (103, 149) 32.7 1100 337 0.95870.9969 Trace
#substs1 714 (695, 731.4) 25.23 1426 328 0.96440.9879 Trace
|A| 174 (161, 199) 84.59 425 920 0.92310.9873 Trace
#indels 58 (50, 67) 6.318 5698 130 0.90911.005 Trace
|indels| 121 (103, 149) 32.7 1100 337 0.95870.9969 Trace
#substs 714 (695, 731.4) 25.23 1426 328 0.96440.9879 Trace
|T| 11.88 (9.365, 15.89) 3.476 10358 171 1.0010.9962 Trace