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

MCMC Post-hoc Analysis: 28 sequences

directory: /home/biodept/br51/Work
subdirectory: few-globins-1
command line: bali-phy few-globins.fasta --smodel=LG+DP[6]

directory: /home/biodept/br51/Work
subdirectory: few-globins-2
command line: bali-phy few-globins.fasta --smodel=LG+DP[6]

directory: /home/biodept/br51/Work
subdirectory: few-globins-3
command line: bali-phy few-globins.fasta --smodel=LG+DP[6]

directory: /home/biodept/br51/Work
subdirectory: few-globins-4
command line: bali-phy few-globins.fasta --smodel=LG+DP[6]

Data & Model

PartitionSequencesLengthsSubstitution ModelIndel Model
1 few-globins.fasta 141 - 190Amino-Acids LG+DP[6] RS07

Analysis

burn-in = 2446 samples sub-sample = 5 P(data|M) = -9470.622 +- 0.675
Complete sample: 7311 topologies 95% Bayesian credible interval: 6109 topologies
chain #Iterations (after burnin)
1 34815 samples
2 22021 samples
3 34482 samples
4 37196 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 1.26% 190 0 (0%) 190 (100%)
Best (WPD) FASTA HTML AU 8.04% 353 2 (0.567%) 229 (64.9%)
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
219277.711249.6290.0110.045 1.0071.019

Scalar variables

StatisticMedian95% BCIACTNeburninPSRF-CI80%PSRF-RCF
prior -877.8 (-938.5, -829.3) 84.25 305 634 0.99641.007 Trace
prior_A1 -688.9 (-746.1, -646.4) 102.8 250 1386 0.9940.9972 Trace
likelihood -9437 (-9468, -9404) 16.6 1548 319 0.99680.9992 Trace
logp -1.032e+04 (-1.037e+04, -1.027e+04) 43.69 588 607 11.008 Trace
Heat.beta 1
Main.mu1 0.4924 (0.3387, 0.739) 1 25706 202 0.99890.9979 Trace
S1.F.piA 0.1177 (0.1052, 0.1306) 6.934 3707 235 11.008 Trace
S1.F.piR 0.02769 (0.02196, 0.03436) 7.849 3275 405 1.0010.9816 Trace
S1.F.piN 0.03791 (0.03136, 0.04532) 6.595 3897 367 1.0031.017 Trace
S1.F.piD 0.05681 (0.04802, 0.06685) 7.825 3285 464 10.9791 Trace
S1.F.piC 0.0139 (0.008979, 0.02026) 6.709 3831 311 0.99951.01 Trace
S1.F.piQ 0.0333 (0.02747, 0.0397) 7.354 3495 508 1.0050.9932 Trace
S1.F.piE 0.05969 (0.05095, 0.06902) 7.943 3236 420 1.0031.012 Trace
S1.F.piG 0.08591 (0.07328, 0.09974) 7.211 3564 497 0.99981.007 Trace
S1.F.piH 0.02676 (0.02134, 0.03328) 6.938 3705 271 0.99760.9969 Trace
S1.F.piI 0.03891 (0.03221, 0.04679) 6.844 3755 292 0.99971.005 Trace
S1.F.piL 0.08793 (0.07487, 0.1023) 7.878 3263 389 1.0020.9993 Trace
S1.F.piK 0.07105 (0.06071, 0.08226) 9.399 2734 269 1.0021.013 Trace
S1.F.piM 0.02338 (0.01832, 0.0293) 7.327 3508 245 1.0011.006 Trace
S1.F.piF 0.0412 (0.03265, 0.05043) 7.901 3253 238 0.99460.9765 Trace
S1.F.piP 0.03838 (0.03041, 0.0469) 7.555 3402 295 10.9853 Trace
S1.F.piS 0.07202 (0.06291, 0.08201) 8.179 3142 202 0.99671.011 Trace
S1.F.piT 0.05416 (0.04586, 0.06291) 7.226 3557 357 1.0020.9925 Trace
S1.F.piW 0.01064 (0.006285, 0.0165) 7.408 3470 769 1.0021.005 Trace
S1.F.piY 0.02399 (0.01801, 0.0311) 8.453 3041 169 1.0071.019 Trace
S1.F.piV 0.07618 (0.06597, 0.08711) 6.807 3776 608 0.98980.9752 Trace
S1.DP.f1[S1] 0.06767 (0.02522, 0.1484) 1.537 16722 227 0.99880.9942 Trace
S1.DP.f2[S1] 0.1579 (0.0511, 0.334) 1.037 24790 96 1.0010.9963 Trace
S1.DP.f3[S1] 0.1805 (0.05724, 0.3581) 1.041 24703 98 0.99860.9916 Trace
S1.DP.f4[S1] 0.178 (0.05826, 0.3578) 1 25706 102 0.99860.9988 Trace
S1.DP.f5[S1] 0.1799 (0.0593, 0.3558) 1.023 25116 138 0.99880.992 Trace
S1.DP.f6[S1] 0.1924 (0.06145, 0.3682) 1 25706 84 0.9980.9979 Trace
S1.DP.rates1[S1] 0.03091 (0.008202, 0.05641) 1.796 14314 183 0.99950.9973 Trace
S1.DP.rates2[S1] 0.09949 (0.06482, 0.1295) 1.312 19590 133 1.0031.009 Trace
S1.DP.rates3[S1] 0.1373 (0.1075, 0.1709) 1.02 25205 195 0.99750.9988 Trace
S1.DP.rates4[S1] 0.1766 (0.142, 0.2233) 1.048 24524 89 1.0021.001 Trace
S1.DP.rates5[S1] 0.2361 (0.1876, 0.2885) 1.095 23482 123 0.99850.9867 Trace
S1.DP.rates6[S1] 0.3152 (0.2607, 0.3844) 1.223 21016 63 1.0011.002 Trace
I1.RS07.logLambda -4.476 (-4.745, -4.222) 1.776 14471 135 1.0021.01 Trace
I1.RS07.meanIndelLength 3.859 (3.159, 4.832) 1.924 13361 168 1.0061.007 Trace
|A1| 345 (319, 365) 330.8 77 2192 0.95581.015 Trace
#indels1 84 (78, 93) 88.36 290 466 0.90.9929 Trace
|indels1| 301 (276, 337) 5.754 4467 320 0.951.004 Trace
#substs1 2045 (2023, 2066) 83.88 306 726 0.95581.008 Trace
|A| 345 (319, 365) 330.8 77 2192 0.95581.015 Trace
#indels 84 (78, 93) 88.36 290 466 0.90.9929 Trace
|indels| 301 (276, 337) 5.754 4467 320 0.951.004 Trace
#substs 2045 (2023, 2066) 83.88 306 726 0.95581.008 Trace
|T| 25.43 (23.03, 28.33) 1.689 15216 193 0.99991.005 Trace