Tree estimation
This directory sets up XML files for BEAST to estimate phylogenies from sequences in the data/ directory. XMLs can be built with the supplied Rakefile.
Statistics
Running ruby scripts/statistics.rb produces statistics from .log files and processed .trees files. Here are mean rates of evolution at first and second position sites and third position sites, as well as effective population sizes across analyses.
| type | pop size | diversity | TMRCA | time to trunk | pos 1&2 rate | pos 3 rate | rate ratio |
|---|---|---|---|---|---|---|---|
| h3_small | 9.2 | 2.87 | 3.21 | 1.39 | 0.003 | 0.0081 | 0.37 |
| h3_large | 15.1 | 3.03 | 3.89 | 1.42 | 0.0032 | 0.0087 | 0.37 |
| h1_small | 12.5 | 4.57 | 4.57 | 3.18 | 0.0027 | 0.0077 | 0.35 |
| h1_large | 16.0 | 4.59 | 4.53 | 3.18 | 0.0028 | 0.0078 | 0.36 |
| vic_small | 20.9 | 5.66 | 5.28 | 2.72 | 0.0013 | 0.0052 | 0.25 |
| vic_large | 21.7 | 5.46 | 5.22 | 2.7 | 0.0014 | 0.0054 | 0.26 |
| yam_small | 16.8 | 6.73 | 7.6 | 2.96 | 0.0013 | 0.0056 | 0.24 |
| yam_large | 17.1 | 6.83 | 7.62 | 3.09 | 0.0014 | 0.0057 | 0.24 |