v3.2.8 (Sep 18 2026)
- Use latexmk to build the PDF documentation, if avaliable.
- Support MCMC chains longer than 2E9 generations.
- Support discrete characters up to 24 states (0-9,A-N
for both unordered and ordered characters). - Support continuous characters with missing states (Brownian motion model).
- Support serially-sampled tips in the coalescent prior.
- Support independent lognormal (ILN) and independent gamma (IGR) clocks.
- Support model averaging (rjMCMC) between ILN and IGR relaxed clock models.
- Renamed the white noise relaxed clock model to WN.
- Updated the parameterization in the TK02 model.
- Updated help messages for the FBD model and parameters.
- Bug fix to the sigma (sd_log) in lnorm rate variation across sites.
- Bug fix to multi-partition Beagle code.
- Bug fix to directional state frequency models.
- Bug fix to erroneous printing of header alpha_symdir.
- Bug fix to setting popsizepr and growthpr for protein data.
- Bug fix to setting ratepr for single partition.
- Better detection of Beagle library in "configure" script.
What's Changed (automatically generated, see above for summary)
- bug fix for BEAGLE on GPU and multiple partitions with mix of invaria… by @ayresdl in #104
- Manual by @nylander in #119
- Spell by @nylander in #120
- Increase size of a couple of string buffers by @andkaha in #121
- add package hyperref for manual by @nylander in #122
- Add documentation relating to installation in Docker containers by @andkaha in #123
- Fixed issue-117 by @andkaha in #126
- Fixed memory reallocation issues when changing number of runs or chains. by @andkaha in #140
- lists of standard moves by @zhangchicool in #129
- white noise relaxed clock by @zhangchicool in #128
- Feature/issue 127 by @ronquist in #141
- Don't allow datatype to be "Continuous" by @andkaha in #142
- Fixed problem with inconsistencies between linking and unlinking of by @ronquist in #144
- Issue-118. by @ronquist in #151
- Fixed bug in sumt for speciestree-genetree analyses by @ronquist in #152
- Invoked printing of the Reallocation of zero size warning again by @ronquist in #153
- Updated the relaxed clock models in the manual by @zhangchicool in #162
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #164
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #165
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #170
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #171
- support unord characters up to 24 states by @zhangchicool in #145
- Cleanup tutorial by @nylander in #181
- Very simple push-checks by @andkaha in #184
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #172
- Feature/issue 154 by @ronquist in #155
- Added explicit definition of ASDSF to manual by @ronquist in #192
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #174
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #175
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #176
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #177
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #178
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #179
- Beagle setup bug by @ronquist in #193
- Feature/issue 186 by @ronquist in #195
- Feature/issue 168 by @ronquist in #197
- Feature/issue 186 again by @andkaha in #199
- Feature/result tests by @andkaha in #198
- Feature/seraina by @ronquist in #200
- Covarion model not supported by Beagle causes crash by @ronquist in #201
- Permissible range of rate values of fixed aarevmatpr too small by @ronquist in #202
- Feature/issue 156 by @ronquist in #204
- Manual by @nylander in #205
- Explicit type conversions to ensure clean compile by @ronquist in #207
- Initialized interiorRoot to NULL to silence compiler warnings by @ronquist in #208
- Feature/issue 58 by @ronquist in #209
- Feature/tap tests by @andkaha in #212
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #221
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #222
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #223
- Update Manual_MrBayes_v3.2.tex by @pablovaldes in #224
- Autotune feature for the rjMCMC clock models by @zhangchicool in #251
- Coalescent prior supporting serially-sampled tips by @zhangchicool in #270
- Fixed issue with checkpointing when root age is calibrated by @ronquist in #285
- Feature/header minor by @zhangchicool in #287
- Fix/smarter disabling by @andkaha in #286
- Fix header guard names by @andkaha in #291
- Better checking of clock tree consistency by @ronquist in #294
- Undefined SSE_ENABLED by default by @zhangchicool in #305
- Feature/continuous traits by @zhangchicool in #310
New Contributors
- @ayresdl made their first contribution in #104
- @pablovaldes made their first contribution in #164
- @zhangchicool with @Copilot made their first contribution in #315
Full Changelog: v3.2.7a...v3.2.8