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.