NEWS

Release Note

v3.2.8 (development version, not yet released)
  * Move to semantic versioning scheme (see https://semver.org/).
    Release numbers are MAJOR.MINOR.PATCH where a new MAJOR release
    number means backward incompatible changes were made, a new MINOR
    number means backward compatible features were added, and a new
    PATCH number means backward compatible bugfixes to the C code were
    made.  We may or may not use transient suffixes like "a", "b",
    "-alpha", "-beta" and "-rcN" as well at times.
  * Use latexmk to build the PDF documentation, if avaliable.
  * Support MCMC chains longer than 2E9 generations.
  * Correct the parameterization sigma (sd_log) in lnorm rate variation across sites.
  * Correct the parameterization in the TK02 model.
  * Renamed the white noise relaxed clock model to WN.
  * Added independent lognormal (ILN) and independent gamma (IGR) relaxed clocks.
  * Support model averaging (rjMCMC) between ILN and IGR clock models.
  * Support unord characters up to 24 states (0-9 A-N).
  * Extend the coalescent prior to support serially-sampled tips.
  * Update help messages for the FBD model and parameters.
  * Bug fix to multi-partition Beagle code.
  * Bug fix to directional state frequency models.
  * Fix erroneous printing of header alpha_symdir.
  * Fix setting popsizepr and growthpr for protein data.
  * Fix disabling variable ratepr for single partition.

v3.2.7a (Mar 06 2019): hotfix
  * PDF manual re-generated from already updated LaTeX sources.

v3.2.7 (Feb 13 2019)
  * Added lognormal and flat ordered dirichelet distributions as
    alternatives to the gamma prior on site variation across sites.
  * Added new, optional moves for the fossilized birth-death model.
  * Added new, optional parsimony-guided moves for non-clock trees.
  * Support for Beagle 3 added.
  * Added support for FMA and AVX instructions in built-in likelihood
    calculators for 4by4 nucleotide models.
  * Added basic command line option support on Unix systems (-h,-i,-v)
  * Various minor bug fixes.

v3.2.6 (Nov 25 2015)
  * Add invertebrate mt, Echinoderm and Euplotid codes [lset code=invermt].
  * Fix a bug of updating branch lengths in tree-stretch move.
  * Correct the proposal ratio in the add/delete branch move.
  * Add more coding options for restriction site chars.

v3.2.5 (Apr 8 2015)
  * Fix pdf in the coalescent prior.
  * Fix a few issues when appending to the previous run.
  * Improve the efficiency of moving ancestral fossils.
  * Add lognormal rate variation among sites [lset rate=lnorm].
  * Add parsimony-biased SPR and TBR proposals (for developers).
  * Other minor bug fixes and improvements.

v3.2.4 (Jan 27 2015)
  * Correct the proposal ratio in the node slider move for non-clock tree.
  * Fix reporting ancestral states under GTR+I+G model.
  * Fix the sliding window in the move of updating omega in codon model.
  * Fix the likelihood and proposal ratio of NaN in the multi-species
    coalescent analysis.
  * Correct screen output messages for a few commands.
  * Fix the interaction of MrBayes with Beagle for the Windows executable.
  * Fix prior pdf of relative rates (rate multipliers).

v3.2.3 (Oct 22 2014)
  * Correct the proposal ratio in the extending TBR move for non-clock tree.
  * Fix numerical error of calculating proposal ratio in
    parsimony-biased SPR moves.
  * Set unconstrained:gammadir prior as default to help avoid
    overestimating branch lengths.
  * Add clock:fossilization prior for total-evidence dating analysis.
  * Add LG model to Aamodelpr [prset aamodelpr=fixed(LG)].
  * Rearrange the code to be more concise.
  * Other minor bug fixes and improvements.

v3.2.2 (Aug 22 2013)
  * Disable LIKE_EPSILON warning for standard users.
  * Fix segmentation fault errors in 64bit version.
  * Fix some issues when dealing with constraints.
  * Fix setting aarevmatpr parameters to fixed for GTR.
  * Other bug fixes and improvements.

v3.2.1 (Feb 8 2012)
v3.2.0 (Nov 16 2011)
  Major release.