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

MCMC Post-hoc Analysis: 28 sequences

Data & Model

PartitionSequencesLengthsAlphabetSubstitution ModelIndel ModelScale Model
1 few-globins.fasta 141 - 190 Amino-Acids LG+F[~DirichletOn[letters[A],1]] + Rates.Gamma[4,~logLaplace[-6,2]] + INV[~Uniform[0,1]] RS07[~Laplace[-4,0.707],Add[1,~Exponential[10]]] ~ Gamma[0.5,2]

Tree Model

topology~ uniform on tree topologies
branch lengths~ iid[num_branches[T],Gamma[0.5,Div[2,num_branches[T]]]]

Analysis

command line: bali-phy few-globins.fasta -S LG+Rates.Gamma+INV

directory: /gpfs/fs0/data/wraycompute/br51/Work/3.0

chain #burninsubsampleIterations (remaining)subdirectory
1 20000 1 180000 few-globins-1
2 20000 1 180000 few-globins-3
3 20000 1 180000 few-globins-4
4 20000 1 180000 few-globins-5
5 20000 1 180000 few-globins-6
6 20000 1 180000 few-globins-7
7 20000 1 180000 few-globins-8

P(data|M) = -9470.376 +- 0.162 Complete sample: 71166 topologies 95% Bayesian credible interval: 29223 topologies

Phylogeny Distribution

Partition support: Summary
Partition support graph: SVG
50% consensusNewick (+PP)PDFSVG
66% consensusNewick (+PP)PDFSVG
80% consensusNewick (+PP)PDFSVG
90% consensusNewick (+PP)PDFSVG
95% consensusNewick (+PP)PDFSVG
99% consensusNewick (+PP)PDFSVG
100% consensusNewick (+PP)PDFSVG
MAPNewick (+PP)PDFSVG
greedyNewick (+PP)PDFSVG

Alignment Distribution

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% 358 2 (0.559%) 229 (64%)
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)ESS (scalar)ESS (partition)ASDSFMSDSFPSRF-CI80%PSRF-RCF
376022659520.4270.0030.012 11.004

Projection of RF distances for the first 3 chains

3D

Variation of split PPs across chains





Scalar variables

StatisticMedian95% BCIACTESSburninPSRF-CI80%PSRF-RCF
prior -600.9 (-654.4, -552.5) 64.41 19562 748 10.9974
prior_A1 -688.6 (-739.5, -643.5) 42.97 29323 506 10.9984
likelihood -9437 (-9469, -9404) 19.88 63381 278 10.9981
logp -1.004e+04 (-1.008e+04, -9997) 54.85 22970 1033 10.9968
Heat.beta 1
Scale[1] 18.69 (13.47, 24.88) 1.11 1135366 178 10.9985
F:pi[A] 0.1175 (0.1049, 0.1304) 8.075 156040 465 0.99991.002
F:pi[R] 0.02772 (0.02177, 0.03406) 8.551 147343 404 11.003
F:pi[N] 0.03785 (0.03112, 0.04499) 8.587 146734 628 10.9994
F:pi[D] 0.05685 (0.04765, 0.06659) 8.549 147385 375 10.9988
F:pi[C] 0.01394 (0.008852, 0.01974) 8.087 155813 417 0.99991.004
F:pi[Q] 0.03321 (0.02708, 0.03953) 8.029 156926 498 11
F:pi[E] 0.05946 (0.0505, 0.06873) 8.757 143887 458 0.99990.9991
F:pi[G] 0.08582 (0.0727, 0.09938) 8.884 141836 441 11.004
F:pi[H] 0.02695 (0.02094, 0.03348) 8.177 154087 411 10.9977
F:pi[I] 0.03898 (0.03169, 0.0466) 8.508 148100 374 0.99990.9949
F:pi[L] 0.08762 (0.07446, 0.1012) 9.882 127504 434 11
F:pi[K] 0.07126 (0.06092, 0.08199) 9.602 131219 417 10.9987
F:pi[M] 0.02379 (0.01847, 0.02956) 8.217 153334 491 10.9977
F:pi[F] 0.04137 (0.03274, 0.05072) 8.402 149973 655 0.99981.001
F:pi[P] 0.03839 (0.03024, 0.04712) 8.433 149409 521 10.9949
F:pi[S] 0.07132 (0.06175, 0.08114) 8.521 147879 362 10.9976
F:pi[T] 0.0541 (0.04588, 0.06252) 8.055 156427 314 11
F:pi[W] 0.01075 (0.006171, 0.01608) 7.846 160585 823 10.9958
F:pi[Y] 0.02416 (0.01793, 0.03098) 8.089 155769 428 11.001
F:pi[V] 0.07642 (0.066, 0.08743) 8.367 150589 623 0.99990.9975
Rates.Gamma:alpha 3.466 (2.47, 4.691) 6.711 187745 153 11.002
INV:pInv 0.01724 (0.001736, 0.04092) 4.065 309998 133 10.9974
RS07:meanIndelLength 3.862 (3.101, 4.762) 9.502 132610 135 11.001
RS07:logLambda -4.447 (-4.712, -4.191) 3.334 377902 135 11.003
|A1| 347 (328, 367) 556.3 2264 3760 0.92530.9768
#indels1 84 (78, 92) 40.1 31421 378 0.90.9984
|indels1| 301 (273, 332) 32.18 39157 550 0.96730.9983
#substs1 2043 (2021, 2063) 197.1 6391 1361 0.93810.9884
Scale1*|T| 24.76 (22.36, 27.37) 2.559 492378 152 10.9997
|A| 347 (328, 367) 556.3 2264 3760 0.92530.9768
#indels 84 (78, 92) 40.1 31421 378 0.90.9984
|indels| 301 (273, 332) 32.18 39157 550 0.96730.9983
#substs 2043 (2021, 2063) 197.1 6391 1361 0.93810.9884
|T| 1.326 (0.9605, 1.739) 1.006 1252160 226 10.9991