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Release Note
After v3.2.7 (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.
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 brls 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.
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