## 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]

- Likelihood rescaling (
- 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.

- Simplify command-line options (
- Fixes
**[3.0-beta2]**Fix compile on XCode 6.