Samples were created by the following command line:
command line: /home/bdredeli/local/bin/bali-phy /home/bdredeli/local/share/bali-phy/examples/Globins/few.fasta --smodel DP[6] --name few-DP6
directory: /brc_share/brc/bdredeli/bdredeli/Globins
| Partition | Sequences | Lengths | Substitution Model | Indel Model |
|---|---|---|---|---|
| 1 | ~/local/share/bali-phy/examples/Globins/few.fasta | 141 - 190 Amino-Acids | [WAG * pi] + rate~Dirichlet[6] | fragment-based indels + T [HMM] |
| burn-in = 9999 samples | after burnin = 90001 samples |
| P(data|M) = -9468.093 +- 0.307 | |
| Complete sample: 9766 topologies | 95% Bayesian credible interval: 4766 topologies |
| Partition support: Summary | Partition support graph: SVG |
| 50% consensus | topology | tree | mtree | SVG | MC Tree (PDF) | MC Tree (SVG) | |
| 66% consensus | topology | tree | mtree | SVG | MC Tree (PDF) | MC Tree (SVG) | |
| 80% consensus | topology | tree | mtree | SVG | MC Tree (PDF) | MC Tree (SVG) | |
| 90% consensus | topology | tree | mtree | SVG | MC Tree (PDF) | MC Tree (SVG) | |
| 95% consensus | topology | tree | mtree | SVG | MC Tree (PDF) | MC Tree (SVG) | |
| 99% consensus | topology | tree | mtree | SVG | MC Tree (PDF) | MC Tree (SVG) | |
| 100% consensus | topology | tree | mtree | SVG | MC Tree (PDF) | MC Tree (SVG) | |
| MAP | topology | tree | SVG |
| Diff | Min. %identity | # Sites | Constant | Variable | Parsimony-Informative | ||||
|---|---|---|---|---|---|---|---|---|---|
| Initial | FASTA | HTML | Diff | 1.26% | 190 | 0 (0%) | 190 (100%) | 190 (100%) | |
| Best (WPD) | FASTA | HTML | AU | 8.04% | 343 | 2 (0.583%) | 341 (99.4%) | 227 (66.2%) | |
| 10% consensus | FASTA | HTML | Diff | AU | 8.21% | 367 | 2 (0.545%) | 365 (99.5%) | 234 (63.8%) |
| 25% consensus | FASTA | HTML | Diff | 9.88% | 367 | 2 (0.545%) | 365 (99.5%) | 234 (63.8%) | |
| 50% consensus | FASTA | HTML | Diff | 16.8% | 375 | 5 (1.33%) | 370 (98.7%) | 228 (60.8%) | |
| 75% consensus | FASTA | HTML | Diff | 41.9% | 499 | 94 (18.8%) | 405 (81.2%) | 222 (44.5%) |
| Statistic | Median | 95% BCI | ACT | Ne | |
|---|---|---|---|---|---|
| prior | -765.8 | (-819.5,-722.6) | 47.15 | 1909 | Trace |
| likelihood | -9435 | (-9467,-9404) | 27.22 | 3306 | Trace |
| logp | -1.02e+04 | (-1.025e+04,-1.016e+04) | 15.42 | 5837 | Trace |
| beta | 1 | ||||
| DP::f1 | 0.02741 | (0.005578,0.0818) | 3.715 | 2.423e+04 | Trace |
| DP::f2 | 0.08695 | (0.004472,0.3452) | 8.702 | 1.034e+04 | Trace |
| DP::f3 | 0.1618 | (0.008066,0.4802) | 9.146 | 9840 | Trace |
| DP::f4 | 0.2077 | (0.009844,0.5084) | 9.21 | 9772 | Trace |
| DP::f5 | 0.2051 | (0.01024,0.496) | 8.599 | 1.047e+04 | Trace |
| DP::f6 | 0.2343 | (0.009099,0.4878) | 8.341 | 1.079e+04 | Trace |
| DP::rate1 | 0.0745 | (0.005969,0.2411) | 5.634 | 1.597e+04 | Trace |
| DP::rate2 | 0.4573 | (0.1521,0.7072) | 7.712 | 1.167e+04 | Trace |
| DP::rate3 | 0.7703 | (0.4668,1.02) | 8.013 | 1.123e+04 | Trace |
| DP::rate4 | 1.059 | (0.7872,1.383) | 5.723 | 1.573e+04 | Trace |
| DP::rate5 | 1.469 | (1.139,1.888) | 5.758 | 1.563e+04 | Trace |
| DP::rate6 | 2.124 | (1.672,2.786) | 9.865 | 9123 | Trace |
| f | 0.9388 | (0.8307,0.9965) | 3.134 | 2.871e+04 | Trace |
| piA | 0.1204 | (0.1073,0.1352) | 5.508 | 1.634e+04 | Trace |
| piR | 0.02716 | (0.0214,0.03392) | 4.416 | 2.038e+04 | Trace |
| piN | 0.0377 | (0.03109,0.04516) | 4.344 | 2.072e+04 | Trace |
| piD | 0.05666 | (0.04752,0.06693) | 5.308 | 1.695e+04 | Trace |
| piC | 0.01287 | (0.008096,0.01919) | 6.547 | 1.375e+04 | Trace |
| piQ | 0.03305 | (0.02711,0.03972) | 3.783 | 2.379e+04 | Trace |
| piE | 0.06005 | (0.05099,0.06991) | 4.995 | 1.802e+04 | Trace |
| piG | 0.08688 | (0.07329,0.102) | 7.751 | 1.161e+04 | Trace |
| piH | 0.0257 | (0.01984,0.03254) | 4.822 | 1.867e+04 | Trace |
| piI | 0.03895 | (0.03178,0.04711) | 4.72 | 1.907e+04 | Trace |
| piL | 0.08861 | (0.07517,0.1032) | 6.654 | 1.353e+04 | Trace |
| piK | 0.07194 | (0.06145,0.08346) | 6.465 | 1.392e+04 | Trace |
| piM | 0.02308 | (0.01795,0.02912) | 4.234 | 2.125e+04 | Trace |
| piF | 0.03989 | (0.0312,0.04989) | 6.373 | 1.412e+04 | Trace |
| piP | 0.03768 | (0.02967,0.04686) | 5.434 | 1.656e+04 | Trace |
| piS | 0.07269 | (0.06299,0.08322) | 4.623 | 1.947e+04 | Trace |
| piT | 0.05419 | (0.04613,0.06326) | 4.191 | 2.147e+04 | Trace |
| piW | 0.01008 | (0.005927,0.01583) | 6.093 | 1.477e+04 | Trace |
| piY | 0.02271 | (0.01663,0.02989) | 5.985 | 1.504e+04 | Trace |
| piV | 0.07678 | (0.06613,0.08856) | 5.344 | 1.684e+04 | Trace |
| lambda | -4.486 | (-4.766,-4.214) | 3.409 | 2.64e+04 | Trace |
| epsilon | -0.2999 | (-0.3814,-0.2321) | 3.512 | 2.563e+04 | Trace |
| invariant | 0.02655 | (0.000961,0.1332) | 1.116 | 8.065e+04 | Trace |
| lambda::prior_median | -5 | ||||
| lambda::prior_stddev | 1.5 | ||||
| epsilon::prior_length | 5 | ||||
| mu | 0.4932 | (0.3743,0.6665) | 1.195 | 7.534e+04 | Trace |
| |A1| | 346 | (328,365) | 82.05 | 1097 | Trace |
| #indels1 | 84 | (78,92) | 56.14 | 1603 | Trace |
| |indels1| | 299 | (274,333) | 13.25 | 6791 | Trace |
| #substs1 | 2044 | (2023,2064) | 35.77 | 2516 | Trace |
| |T| | 25.7 | (23.25,28.6) | 2.88 | 3.125e+04 | Trace |
