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

MCMC Post-hoc Analysis: 28 sequences

Data & Model

PartitionSequencesLengthsAlphabetSubstitution ModelIndel ModelScale Model
1 few-globins.fasta 141 - 190 Amino-AcidsS1 = lg08+f+Rates.free[,,5] I1 = rs07 scale1 ~ gamma[0.5,2,0.0]

Scalar variables

StatisticMedian95% BCIACTESSburninPSRF-CI80%PSRF-RCF
prior -613.3 (-665.9, -565.4) 52.27 27550 546 11.001
prior_A1 -687.9 (-737.8, -643.9) 30.76 46821 511 10.9998
likelihood -9437 (-9468, -9405) 14.62 98510 267 10.9989
posterior -1.005e+04 (-1.01e+04, -1.001e+04) 47.41 30371 527 11.001
Heat.beta 1
Scale[1] 18.73 (13.5, 24.91) 1.114 1293017 97 11.001
f:pi[A] 0.1176 (0.1049, 0.1305) 8.036 179197 417 10.9978
f:pi[R] 0.02774 (0.02181, 0.03407) 7.962 180856 597 10.9982
f:pi[N] 0.03775 (0.03092, 0.04484) 8.343 172597 752 11.007
f:pi[D] 0.05673 (0.04747, 0.06638) 8.624 166971 543 11
f:pi[C] 0.01395 (0.008829, 0.01973) 8.123 177282 366 10.9966
f:pi[Q] 0.03315 (0.02712, 0.03956) 8.32 173085 472 0.99990.9987
f:pi[E] 0.05943 (0.05054, 0.06868) 8.839 162919 338 10.9973
f:pi[G] 0.08618 (0.07299, 0.09971) 8.592 167590 467 0.99990.9956
f:pi[H] 0.02686 (0.02087, 0.0333) 8.084 178131 288 11.003
f:pi[I] 0.03898 (0.03174, 0.04665) 8.49 169613 297 11.002
f:pi[L] 0.08829 (0.07516, 0.102) 8.999 160020 602 11.001
f:pi[K] 0.07095 (0.06064, 0.08171) 9.067 158816 433 0.99991.001
f:pi[M] 0.02342 (0.0181, 0.0291) 8.241 174744 644 11.003
f:pi[F] 0.0412 (0.03246, 0.05043) 8.431 170805 351 10.9975
f:pi[P] 0.03843 (0.03015, 0.04709) 8.432 170782 341 0.99991.002
f:pi[S] 0.07179 (0.06223, 0.08172) 8.384 171755 308 11
f:pi[T] 0.05407 (0.04592, 0.06257) 7.965 180784 368 11.003
f:pi[W] 0.01075 (0.006137, 0.01604) 7.914 181952 508 11
f:pi[Y] 0.02406 (0.01779, 0.03089) 8.145 176793 609 11.003
f:pi[V] 0.07612 (0.06549, 0.08701) 8.609 167261 403 10.9985
Rates.free:frequencies[1] 0.06663 (0.01614, 0.1426) 13.14 109579 327 0.99991.001
Rates.free:frequencies[2] 0.1919 (0.03648, 0.3928) 6.662 216148 375 10.9998
Rates.free:frequencies[3] 0.2302 (0.0483, 0.4357) 4.527 318070 382 11.001
Rates.free:frequencies[4] 0.2235 (0.0469, 0.4248) 4.056 355073 428 11.002
Rates.free:frequencies[5] 0.2524 (0.06324, 0.4427) 5.96 241628 286 10.9989
Rates.free:rates[1] 0.03833 (0.008093, 0.06836) 13.95 103260 495 11.001
Rates.free:rates[2] 0.1299 (0.08633, 0.1688) 9.623 149649 390 11.003
Rates.free:rates[3] 0.1876 (0.1469, 0.2325) 4.269 337303 291 10.9998
Rates.free:rates[4] 0.2601 (0.2065, 0.3262) 5.821 247399 404 10.9998
Rates.free:rates[5] 0.3801 (0.3105, 0.4522) 9.173 156990 260 11
rs07:mean_length 3.865 (3.102, 4.767) 12.4 116172 240 10.9988
rs07:log_rate -4.452 (-4.715, -4.197) 2.667 539868 250 10.9979
|A1| 347 (325, 365) 747.9 1925 4350 0.93880.9806
#indels1 84 (77, 91) 30.48 47242 546 0.87671
|indels1| 301 (273, 332) 44.14 32624 585 0.96510.9953
#substs1 2043 (2021, 2063) 287.1 5015 3108 0.98180.9901
Scale1*|T| 24.83 (22.44, 27.35) 2.623 548967 207 11
|A| 347 (325, 365) 747.9 1925 4350 0.93880.9806
#indels 84 (77, 91) 30.48 47242 546 0.87671
|indels| 301 (273, 332) 44.14 32624 585 0.96510.9953
#substs 2043 (2021, 2063) 287.1 5015 3108 0.98180.9901
|T| 1.327 (0.9622, 1.739) 1.018 1415236 174 11.001

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 8.04% 356 2 (0.562%) 227 (63.8%)
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
435019259958.8240.0040.016 11.007

Projection of RF distances for the first 3 chains (Hillis et al 2005)

3D

Variation of split PPs across chains (Beiko et al 2006)







Analysis

command line: bali-phy few-globins.fasta -S LG+Rates.free[n=5] --name few-globins-free5

directory: /gpfs/fs0/data/wraycompute/br51/Work/3.1

chain #burninsubsampleIterations (after burnin)subdirectory
1 20000 1 180000 few-globins-free5-1
2 20000 1 180000 few-globins-free5-2
3 20000 1 180000 few-globins-free5-3
4 20000 1 180000 few-globins-free5-4
5 20000 1 180000 few-globins-free5-5
6 20000 1 180000 few-globins-free5-6
7 20000 1 180000 few-globins-free5-7
8 20000 1 180000 few-globins-free5-8

P(data|M) = -9469.685 +- 0.197 Complete sample: 75423 topologies 95% Bayesian credible interval: 29187 topologies

Model and priors

Tree (+priors)

topology~ uniform on tree topologies
branch lengths~ iid[num_branches[T],gamma[0.5,div[2,num_branches[T]],0.0]]

Substitution model (+priors)

S1= lg08+f+Rates.free[,,5]
f:pi~dirichlet_on[letters[A],1]
Rates.free:rates~dirichlet[n,2]
Rates.free:frequencies~dirichlet[n,3]

Indel model (+priors)

I1= rs07
rs07:log_rate~laplace[-4,0.707]
rs07:mean_length~exponential[10,1]

Scales (+priors)

scale1~ gamma[0.5,2,0.0]