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@kusalananda kusalananda released this Jan 10, 2020

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).

Assets 4

@nylander nylander released this Jan 10, 2020

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.
Assets 5

@nylander nylander released this Jan 10, 2020

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.
Assets 5

@nylander nylander released this Jan 10, 2020

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).
Assets 5

@kusalananda kusalananda released this Jan 17, 2020

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

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

Assets 3

@nylander nylander released this Jun 15, 2018

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.
Assets 5

@nylander nylander released this Jun 15, 2018

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.
Assets 5

@nylander nylander released this Jun 15, 2018

v3.2.1 (Feb 8 2012)

  • Hotfix
Assets 6

@nylander nylander released this Jun 15, 2018

v3.2.0 (Nov 16 2011)

  • Major release.
Assets 6