Samples were created by the following command line:
command line: /home/bdredeli/local-2.0/bin/bali-phy /home/bdredeli/local/share/bali-phy/examples/5S-rRNA/25-muscle.fasta --smodel GTR+log-normal[8] --iterations 400000 --name 25-log-normal-B
directory: /brc_share/brc/bdredeli/bdredeli/5S
| Partition | Sequences | Lengths | Substitution Model | Indel Model |
|---|---|---|---|---|
| 1 | ~/local/share/bali-phy/examples/5S-rRNA/25-muscle.fasta | 111 - 131 RNA nucleotides | [GTR * pi] + rate~LogNormal(8) | fragment-based indels + T [HMM] |
| burn-in = 39999 samples | after burnin = 360001 samples |
| P(data|M) = -2731.434 +- 0.220 | |
| Complete sample: 311134 topologies | 95% Bayesian credible interval: 293134 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 | 33.9% | 135 | 8 (5.93%) | 127 (94.1%) | 113 (83.7%) | |
| Best (WPD) | FASTA | HTML | AU | 32.2% | 171 | 11 (6.43%) | 160 (93.6%) | 125 (73.1%) | |
| 10% consensus | FASTA | HTML | Diff | AU | 30.6% | 182 | 11 (6.04%) | 171 (94%) | 124 (68.1%) |
| 25% consensus | FASTA | HTML | Diff | 33.1% | 182 | 14 (7.69%) | 168 (92.3%) | 124 (68.1%) | |
| 50% consensus | FASTA | HTML | Diff | 34.7% | 202 | 32 (15.8%) | 170 (84.2%) | 121 (59.9%) | |
| 75% consensus | FASTA | HTML | Diff | 56.2% | 349 | 182 (52.1%) | 167 (47.9%) | 120 (34.4%) |
| Statistic | Median | 95% BCI | ACT | Ne | |
|---|---|---|---|---|---|
| prior | -491.4 | (-552.9,-442.4) | 39.06 | 9217 | Trace |
| likelihood | -2701 | (-2730,-2672) | 46.91 | 7674 | Trace |
| logp | -3193 | (-3246,-3152) | 22.44 | 1.604e+04 | Trace |
| beta | 1 | ||||
| mu | 0.3658 | (0.227,0.6527) | 10.01 | 3.595e+04 | Trace |
| GTR::AG | 0.189 | (0.1423,0.242) | 5.492 | 6.555e+04 | Trace |
| GTR::AT | 0.2166 | (0.1601,0.2899) | 4.784 | 7.525e+04 | Trace |
| GTR::AC | 0.05357 | (0.02506,0.09062) | 4.146 | 8.683e+04 | Trace |
| GTR::GT | 0.08516 | (0.04954,0.1275) | 22.65 | 1.589e+04 | Trace |
| GTR::GC | 0.09054 | (0.05231,0.1364) | 20.33 | 1.771e+04 | Trace |
| GTR::TC | 0.3586 | (0.296,0.4261) | 9.806 | 3.671e+04 | Trace |
| f | 0.2502 | (0.009917,0.8946) | 2.398 | 1.501e+05 | Trace |
| piA | 0.2022 | (0.168,0.2433) | 9.735 | 3.698e+04 | Trace |
| piG | 0.32 | (0.2741,0.3687) | 6.496 | 5.542e+04 | Trace |
| piU | 0.1875 | (0.1597,0.2197) | 26.63 | 1.352e+04 | Trace |
| piC | 0.288 | (0.2487,0.3306) | 13.42 | 2.684e+04 | Trace |
| log-normal::sigma/mu | 2.202 | (1.44,3.855) | 10.41 | 3.458e+04 | Trace |
| lambda | -4.24 | (-4.83,-3.746) | 10.71 | 3.361e+04 | Trace |
| epsilon | -0.6314 | (-0.8774,-0.4343) | 72.31 | 4979 | Trace |
| invariant | 0.0265 | (0.0009775,0.1324) | 1.131 | 3.184e+05 | Trace |
| lambda::prior_median | -5 | ||||
| lambda::prior_stddev | 1.5 | ||||
| epsilon::prior_length | 5 | ||||
| |A| | 172 | (161,195) | 485.2 | 742 | Trace |
| #indels | 57 | (50,67) | 34.14 | 1.055e+04 | Trace |
| |indels| | 118 | (101,146) | 153 | 2352 | Trace |
| #substs | 711 | (693,728) | 107.2 | 3359 | Trace |
| |T| | 16.71 | (11.45,28.02) | 13.06 | 2.756e+04 | Trace |
