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

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]

Data & Model

PartitionSequencesLengthsSubstitution ModelIndel Model
1 48-fsa.fasta 110 - 131RNA nucleotides GTR+DP[4] RS07

Analysis

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

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 17.7% 214 6 (2.8%) 187 (87.4%)
Best (WPD) FASTA HTML AU 28.5% 212 8 (3.77%) 157 (74.1%)
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
4331672654.9920.0100.026 1.0051.017

Scalar variables

StatisticMedian95% BCIACTNeburninPSRF-CI80%PSRF-RCF
prior -1038 (-1110, -973.9) 5.035 3048 163 0.99950.9989 Trace
prior_A1 -754.9 (-820, -700.4) 2.532 6061 161 1.0051.005 Trace
likelihood -4041 (-4082, -3999) 3.034 5058 174 1.0011.016 Trace
logp -5079 (-5139, -5025) 4.465 3437 143 1.0041.01 Trace
Heat.beta 1
Main.mu1 0.1603 (0.1135, 0.2327) 1.316 11661 220 1.0011.002 Trace
S1.GTR.ag 0.2004 (0.1541, 0.2518) 1.509 10170 101 0.99910.9949 Trace
S1.GTR.at 0.2356 (0.1797, 0.2975) 3.071 4998 199 0.99981 Trace
S1.GTR.ac 0.06871 (0.04213, 0.1008) 1.276 12032 139 11.009 Trace
S1.GTR.gt 0.04227 (0.0201, 0.0703) 1.677 9151 170 10.9962 Trace
S1.GTR.gc 0.08834 (0.06095, 0.1226) 1.999 7676 162 0.99831.005 Trace
S1.GTR.tc 0.36 (0.2973, 0.4285) 1.714 8956 167 1.0010.9969 Trace
S1.F.piA 0.2114 (0.1794, 0.2487) 1.802 8517 107 11.009 Trace
S1.F.piG 0.2949 (0.253, 0.3379) 1.993 7700 163 0.99951.006 Trace
S1.F.piU 0.2134 (0.1848, 0.2455) 2.084 7363 108 1.0021.008 Trace
S1.F.piC 0.2786 (0.2453, 0.3147) 1.245 12325 101 10.9935 Trace
S1.DP.f1[S1] 0.1994 (0.1248, 0.286) 1.311 11711 109 1.0041.003 Trace
S1.DP.f2[S1] 0.3203 (0.1267, 0.4655) 1.446 10611 79 1.0020.9893 Trace
S1.DP.f3[S1] 0.27 (0.1054, 0.4183) 1.211 12678 170 0.99881.006 Trace
S1.DP.f4[S1] 0.2178 (0.07536, 0.3739) 2.295 6686 127 10.998 Trace
S1.DP.rates1[S1] 0.008341 (0.002243, 0.02007) 1.462 10494 123 1.0011.005 Trace
S1.DP.rates2[S1] 0.111 (0.07307, 0.1646) 2.127 7214 146 1.0010.9983 Trace
S1.DP.rates3[S1] 0.2623 (0.1927, 0.3526) 1 15348 103 0.99930.9919 Trace
S1.DP.rates4[S1] 0.6161 (0.5132, 0.698) 1.212 12660 114 0.9990.9923 Trace
I1.RS07.logLambda -3.565 (-3.889, -3.257) 2.059 7454 129 1.0020.9993 Trace
I1.RS07.meanIndelLength 1.949 (1.632, 2.384) 2.439 6293 165 0.99990.9945 Trace
|A1| 201 (187, 217) 9.179 1672 200 0.94741.016 Trace
#indels1 101 (91, 112) 2.898 5296 104 0.87271.008 Trace
|indels1| 189 (166, 217) 4.965 3091 433 0.97711.013 Trace
#substs1 1023 (1002, 1047) 6.03 2545 206 0.96671.017 Trace
|A| 201 (187, 217) 9.179 1672 200 0.94741.016 Trace
#indels 101 (91, 112) 2.898 5296 104 0.87271.008 Trace
|indels| 189 (166, 217) 4.965 3091 433 0.97711.013 Trace
#substs 1023 (1002, 1047) 6.03 2545 206 0.96671.017 Trace
|T| 14.64 (11.97, 18.34) 2.234 6868 163 0.9970.9929 Trace