Release Notes

Version 3 (in development):
  • [3.0-beta1] - May-05-2017
  • [3.0-beta2] - Jul-13-2017
  • Speed & Memory
    • [65%-300% faster] Rewrite core.
    • [0%-300% less memory] Rewrite core.
    • [3.0-beta2] Decrease memory use for large trees.
  • Features
    • Likelihood rescaling (compute likelihoods for large trees).
    • New treelength prior: don't prefer huge treelengths for trees with lots of leaves.
    • Allow analyzing 1- and 2-sequence alignments.
    • Print out the model and priors (including defaults)
    • Allow specifying priors for substitution model and indel model,
      • --smodel=HKY[kappa=2].
      • --imodel=RS07[logLambda~Laplace[-4,0.707],meanIndelLengthMinus1~Exponential[10]]
    • Allow specifying priors on scale factors for branch lengths in each partition:
      • --scale=~Gamma[0.5,2]
      • --scale=1
    • Allow specifying priors on branch lengths.
      • --branch-length=~Gamma[0.5,0.1]
  • Misc
    • Add unit tests.
    • [3.0-beta2] Expand likelihood testsuite.
  • Summarization tools
    • [3.0-beta2] bp-analyze.pl - Beautify and condense MCMC statistics.
    • [3.0-beta2] bp-analyze.pl - Show MDS topology convergence figures.
    • [3.0-beta2] bp-analyze.pl - Don't compute trace plots (too slow, large files).
  • Changes
    • Simplify command-line options (some old options have been removed).
    • Change spelling for Gamma to GammaRates: GTR+Gamma+INV -> GTR+GammaRates+INV
    • [3.0-beta2] Suffix parameter files with *.log instead of *.p to match other software.
  • Fixes
    • [3.0-beta2] Fix compile on XCode 6.

comments and suggestions: benjamin . redelings * gmail + com