BAli---Phy

Release Notes

• Speed & Memory
  • [65%-300% faster] Rewrite core.
  • [0%-300% less memory] Rewrite core.
  • [3.0-beta2] Decrease memory use for large trees.
  • [3.0-beta3] Decrease memory use up to 3-fold.
  • [3.0-beta3] 7-15% faster.
• 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.