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

MCMC Post-hoc Analysis: 68 sequences

Data & Model

PartitionSequencesLengthsAlphabetSubstitution ModelIndel ModelScale Model
1 ITS1-trimmed.fasta 198 - 210 DNAS1 = tn93+Rates.free[,,3] I1 = rs07 scale1 ~ gamma[0.5,2,0.0]
2 5.8S.fasta 15 - 16 DNAS2 = tn93 none scale2 ~ gamma[0.5,2,0.0]
3 ITS2-trimmed.fasta 154 - 159 DNAS1 = tn93+Rates.free[,,3] I2 = rs07 scale1 ~ gamma[0.5,2,0.0]

Scalar variables

StatisticMedian95% BCIACTESSburninPSRF-CI80%PSRF-RCF
prior -92.02 (-144.6, -41.7) 15.15 62439 202 0.99991.001
prior_A1 -404.6 (-434.9, -379) 6.26 151133 305 11.005
prior_A3 -198.9 (-223.2, -180.5) 29.83 31714 243 10.999
likelihood -2967 (-2998, -2936) 20.55 46048 458 11.002
posterior -3059 (-3106, -3014) 6.103 155018 175 0.99981.002
Heat.beta 1
Scale[1] 1.12 (0.8317, 1.467) 1.254 754205 208 0.99990.9981
Scale[2] 0.07923 (0.03648, 0.1333) 1 946098 88 10.9996
S1/tn93:pi[A] 0.1846 (0.1552, 0.2146) 3.541 267217 324 0.99971.002
S1/tn93:pi[C] 0.313 (0.2775, 0.3489) 3.384 279614 216 10.9991
S1/tn93:pi[G] 0.2712 (0.237, 0.3073) 4.05 233607 202 10.9975
S1/tn93:pi[T] 0.2302 (0.1992, 0.2623) 3.545 266858 277 10.9976
S1/tn93:kappaPyr 3.985 (3.073, 4.998) 2.258 419085 132 10.9992
S1/tn93:kappaPur 2.703 (2.008, 3.506) 1.755 539192 107 10.9999
S1/Rates.free:frequencies[1] 0.4485 (0.1773, 0.658) 9.835 96193 299 11.001
S1/Rates.free:frequencies[2] 0.2686 (0.06417, 0.4905) 4.897 193214 265 10.9998
S1/Rates.free:frequencies[3] 0.3008 (0.08767, 0.4654) 8.672 109092 462 11
S1/Rates.free:rates[1] 0.05259 (0.01176, 0.1016) 7.26 130317 395 1.0010.9994
S1/Rates.free:rates[2] 0.2368 (0.08345, 0.4381) 12.4 76292 400 0.99981.004
S1/Rates.free:rates[3] 0.7145 (0.503, 0.8532) 11.57 81745 493 0.99981.005
S2/tn93:pi[A] 0.2448 (0.1833, 0.3111) 2.699 350589 208 0.99991.002
S2/tn93:pi[C] 0.2408 (0.179, 0.3058) 2.74 345240 326 10.9969
S2/tn93:pi[G] 0.245 (0.1825, 0.3105) 2.713 348691 249 0.99991.002
S2/tn93:pi[T] 0.2655 (0.2012, 0.3324) 2.718 348083 203 0.99981.002
S2/tn93:kappaPyr 2.762 (1.646, 4.185) 1.048 902444 121 11
S2/tn93:kappaPur 1.815 (1.069, 2.76) 1.041 908761 152 11
I1/rs07:mean_length 1.268 (1.118, 1.458) 1.733 545898 206 10.9998
I1/rs07:log_rate -2.196 (-2.529, -1.868) 2.156 438830 167 0.99980.999
I2/rs07:mean_length 1.096 (1.002, 1.275) 4.007 236102 197 10.9978
I2/rs07:log_rate -2.705 (-3.178, -2.258) 3.753 252106 164 10.995
|A1| 242 (239, 246) 107.3 8818 473 0.81.006
#indels1 52 (47, 56) 4.165 227153 169 0.83331.002
|indels1| 65 (59, 71) 5.473 172856 352 0.88891.002
#substs1 210 (204, 215) 44.49 21265 248 0.85711.001
#substs2 12 (12, 12) 1.134 834478 6 10.9998
|A3| 171 (169, 173) 82.85 11419 382 0.640.9979
#indels3 25 (22, 28) 24.22 39066 116 0.750.9996
|indels3| 26 (23, 30) 15.81 59846 126 0.751.001
#substs3 154 (149, 159) 8.522 111021 182 0.85710.9986
Scale1*|T| 1.102 (0.9472, 1.269) 1.924 491680 118 0.99990.9986
Scale2*|T| 0.07795 (0.03826, 0.125) 1.026 922056 159 10.9963
|A| 430 (425, 434) 143.6 6590 546 0.74421.003
#indels 79 (73, 84) 12.89 73426 263 0.8751.002
|indels| 94 (87, 101) 12.28 77070 371 0.91141.002
#substs 377 (369, 384) 25.99 36399 371 0.91
|T| 0.9841 (0.7546, 1.229) 1 946098 176 0.99990.9985

Phylogeny Distribution

Partition support: SummaryAcross chains
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 68.9% 223 93 (41.7%) 93 (41.7%)
Best (WPD) FASTA HTML AU 69.4% 243 92 (37.9%) 99 (40.7%)

Partition 2

Diff Min. %identity # Sites Constant Informative
Initial FASTA HTML 68.8% 16 4 (25%) 5 (31.2%)

Partition 3

Diff Min. %identity # Sites Constant Informative
Initial FASTA HTML Diff 74.4% 172 77 (44.8%) 75 (43.6%)
Best (WPD) FASTA HTML AU 78.6% 171 80 (46.8%) 62 (36.3%)

Mixing

Statistics:

scalar burnin546
scalar ESS6591
topological ESS1400.757
ASDSF0.002
MSDSF0.016
PSRF CI80%1.001
PSRF RCF1.006
SRQ plot for supprt of 50% consensus tree. SRQ plot for support of each partition.

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 -c ITS.txt --name ITS-3.1.5
directory: /gpfs/fs0/data/wraycompute/br51/Work/3.1
version: 3.1.5

chain #burninsubsampleIterations (after burnin)subdirectory
1 10957 1 146913 ITS-3.1.5-1
2 10957 1 111407 ITS-3.1.5-2
3 10957 1 119290 ITS-3.1.5-3
4 10957 1 116229 ITS-3.1.5-4
5 10957 1 120336 ITS-3.1.5-5
6 10957 1 118486 ITS-3.1.5-6
7 10957 1 114788 ITS-3.1.5-7
8 10957 1 98615 ITS-3.1.5-8

P(data|M) = -2999.712 +- 0.366 Complete sample: 1034060 topologies 95% Bayesian credible interval: 982357 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= tn93+Rates.free[,,3]
tn93:kappaPur~log_normal[log[2],0.25]
tn93:kappaPyr~log_normal[log[2],0.25]
tn93:pi~dirichlet_on[letters[a],1]
Rates.free:rates~dirichlet[n,2]
Rates.free:frequencies~dirichlet[n,3]
S2= tn93
tn93:kappaPur~log_normal[log[2],0.25]
tn93:kappaPyr~log_normal[log[2],0.25]
tn93:pi~dirichlet_on[letters[a],1]

Indel model (+priors)

I1= rs07
rs07:log_rate~laplace[-4,0.707]
rs07:mean_length~exponential[10,1]
I2= rs07
rs07:log_rate~laplace[-4,0.707]
rs07:mean_length~exponential[10,1]

Scales (+priors)

scale1~ gamma[0.5,2,0.0]
scale2~ gamma[0.5,2,0.0]