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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