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

MCMC Post-hoc Analysis: 48 sequences

Data & Model

PartitionSequencesLengthsAlphabetSubstitution ModelIndel ModelScale Model
1 48-fsa.fasta 110 - 131 RNAS1 = gtr+Rates.gamma[4]+inv I1 = rs07 scale1 ~ gamma[0.5,2,0.0]

Scalar variables

StatisticMedian95% BCIACTESSburninPSRF-CI80%PSRF-RCF
prior -470.3 (-537.4, -406.5) 26.66 53770 279 10.9995
prior_A1 -754.2 (-817.1, -696.4) 27.41 52302 279 10.9985
likelihood -4041 (-4082, -4000) 35.26 40651 237 10.9982
posterior -4511 (-4568, -4459) 13.74 104298 228 10.9985
Heat.beta 1
Scale[1] 12.36 (8.833, 16.54) 4.88 293739 180 11.002
gtr:pi[A] 0.2127 (0.1782, 0.2496) 25.04 57239 572 11.001
gtr:pi[C] 0.2822 (0.2475, 0.3183) 13.43 106764 273 11.001
gtr:pi[G] 0.2879 (0.2468, 0.3314) 29.92 47899 332 11
gtr:pi[U] 0.2152 (0.1844, 0.2469) 28.73 49886 1017 11.003
gtr:sym[AC] 0.06996 (0.04235, 0.1) 9.525 150483 353 11.003
gtr:sym[AG] 0.205 (0.1577, 0.2554) 18.73 76526 849 10.9987
gtr:sym[AU] 0.232 (0.1757, 0.2922) 35.56 40311 886 11.001
gtr:sym[CG] 0.09082 (0.06181, 0.1233) 28.22 50790 1020 11.005
gtr:sym[CU] 0.3511 (0.2876, 0.4173) 23.65 60595 526 10.9992
gtr:sym[GU] 0.04625 (0.02222, 0.0729) 13.07 109695 437 10.9984
Rates.gamma:alpha 1.328 (0.7789, 1.873) 12.65 113293 374 0.99991.001
inv:p_inv 0.1436 (0.06041, 0.2317) 9.495 150956 205 0.99991.002
rs07:mean_length 1.954 (1.608, 2.355) 20.13 71188 389 0.99981.001
rs07:log_rate -3.504 (-3.812, -3.207) 14.41 99487 403 11.001
|A1| 201 (186, 215) 169.3 8465 2829 0.96820.99
#indels1 101 (90, 111) 26.78 53528 265 0.92860.998
|indels1| 189 (163, 213) 49.61 28892 518 0.97340.9955
#substs1 1023 (1001, 1045) 46.77 30648 611 0.97070.9976
Scale1*|T| 13.75 (11.24, 16.63) 14.13 101470 322 0.99981.002
|A| 201 (186, 215) 169.3 8465 2829 0.96820.99
#indels 101 (90, 111) 26.78 53528 265 0.92860.998
|indels| 189 (163, 213) 49.61 28892 518 0.97340.9955
#substs 1023 (1001, 1045) 46.77 30648 611 0.97070.9976
|T| 1.116 (0.8416, 1.415) 1.017 1409462 71 10.9999

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 17.7% 214 6 (2.8%) 187 (87.4%)
Best (WPD) FASTA HTML AU 25.8% 206 8 (3.88%) 152 (73.8%)
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
2829846510999.3250.0070.024 11.005

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 48-fsa.fasta -S gtr+Rates.gamma+inv

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

chain #burninsubsampleIterations (after burnin)subdirectory
1 19236 1 180764 48-fsa-1
2 19236 1 180764 48-fsa-2
3 19236 1 180764 48-fsa-3
4 19236 1 180764 48-fsa-4
5 19236 1 173128 48-fsa-5
6 19236 1 180764 48-fsa-6
7 19236 1 180084 48-fsa-7
8 19236 1 176297 48-fsa-8

P(data|M) = -4085.760 +- 0.389 Complete sample: 1586668 topologies 95% Bayesian credible interval: 1507308 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= gtr+Rates.gamma[4]+inv
gtr:sym~dirichlet_on[letter_pairs[a],1]
gtr:pi~dirichlet_on[letters[a],1]
Rates.gamma:alpha~log_laplace[6,2]
inv:p_inv~uniform[0,1]

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]