v3.2.7

News:

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.

Note March 20: Windows binaries are provisional (without beagle).

v3.2.6

v3.2.6 (Nov 25 2015)

• Added invertebrate mt, Echinoderm and Euplotid codes [lset code=invermt].
• Fixed a bug of updating brls in tree-stretch move.
• Corrected the proposal ratio in the add/delete branch move.
• Added more coding options for restriction site chars.

v3.2.5

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

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).

v3.2.7a

Hotfix, minor: Regenerated PDF manual from already updated sources.

This should be the "latest release" (as of May 2020)

v3.2.3

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

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

v3.2.1 (Feb 8 2012)

• Hotfix

v3.2.0

v3.2.0 (Nov 16 2011)

• Major release.