                    BEAST v1.5.2 2002-2009
        Bayesian Evolutionary Analysis Sampling Trees
                              by
      Alexei J. Drummond, Andrew Rambaut & Marc Suchard

                Department of Computer Science
                     University of Auckland
                    alexei@cs.auckland.ac.nz

              Institute of Evolutionary Biology
                    University of Edinburgh
                      a.rambaut@ed.ac.uk

               David Geffen School of Medicine
            University of California, Los Angeles
                      msuchard@ucla.edu


Version History
Last updated: alexei@cs.auckland.ac.nz - 9th October 2009

================================================================================

Version 1.5.2 released 9th October 2009

    Bug Fixes
		Many bugs fixed that were introduced in 1.5.1 including:

        Issue 44: Recent change (svn commit 773) breaks Beauti
        Issue 75: "Unlink substitution model across codon positions has no effect
        Issue 77: BEAUti v1.5 produces decimal operator weights that don't work with
                  old BEAST
        Issue 94: Improve the prefix of PartitionClockModelTreeModelLink
        Issue 123: BEAUti uses a poor choice of name for re-linking partitions  
        Issue 131: BEAUTi: rewrite Parameter and Operator class by Builder pattern,
                   and all referring methods
        Issue 134: TN93 parser problem
        Issue 135: Laplace prior has not been implemented in PriorParsers, but
                   appearing in BEAUTi.
        Issue 136: BEAUTi log screen should show actual name instead of Rate 1, 2, ....
        Issue 139: ImportnaceNarrowExchange should be ImportanceNarrowExchange
        Issue 140: more options for *beast
        Issue 144: BEAUTi: "In use" in Operators panel cannot be changed for those
                   operators belonging to PartitionClockModelTreeModelLink  
        Issue 145: BEAUTi: implement frequencies for binary model in the same way as
                   for DNA data
        Issue 147: BEAUTi: if no leaf nodes selected in Taxon Set panel, the
                   corresponding tmrca should not appear in Prior panel
        Issue 148: BEAUTi: illegal entry error for Clock Model panel
        Issue 151: BEAUti: MCMC tab numerical fields reset after GUI events
        Issue 154: No Nucleotide Likelihood Core in java.library.path
        Issue 155: Warning message " ... does not match stored object with same id
                   and tag name ..." confused user
        Issue 156: LogNormal in prior panel in Beauti
        Issue 157: LogNormal in Beauti: Exception occurred during event dispatching
        Issue 158: We should have the Inverse Gamma distribution in Beauti
        Issue 160: Ant build for Mac version release
        Issue 163: BEAUTi: unlink trees if allow different taxa
        Issue 164: TreeAnnotator v1.5.1 incorrectly labels tree [bug report AND fix
                   solution!]
        Issue 165: BEAUTi: some priors parameters keep changing
        Issue 168: GMRF 'Skyride' complains about 'Share same tree prior' even if only
                   one tree
        Issue 172: BEAUti: shareSameTreePrior should be disabled when there is only 1
                   tree model
        Issue 176: BEAUti: LogNormal mean should be > 0 when mean in real space
        Issue 179: species.popSize is a horrible choice of name
        Issue 180: BEAUTi: allMus is not dealing with multi-partition + codon, and
                   allClockRate
        Issue 183: BEAUTi: clock model should use different mu with codon model
        Issue 184: BEAUTi: make "mu" only appeared using codon model
        Issue 185: Guess Trait dialog doesn't offer user defined traits
        Issue 188: Suggestion to remove 'pre-burnin'
        Issue 190: Mac app ant build needs several corrections
        Issue 192: BEAUti: GUI exception when attempting to add a new trait 
        Issue 195: BEAUTi ignores and resets change of prior
        Issue 196: Beast failure with file generated by BEAUTi (ucld)
        Issue 197: meanRate, coefficientOfVariation and covariance should have gene name
                   in name="" attribute
        Issue 200: BEAUTi: *BEAST using Import Trait cannot add species in Trait table

        All issues can be viewed at http://code.google.com/p/beast-mcmc/issues/list

================================================================================

Version 1.5.1 released 3rd September 2009

	New Features:
	    *BEAST: a version of BEAST that can estimate species trees from
	    multi-locus multi-individual data sets using the multispecies coalescent
	    (Heled & Drummond, 2009, submitted)

	    BEAUti overhaul: BEAUti has been completely re-written to allow flexible
	    handling of multi-partition analyses, including partitioning by
	    substitution models, clock models and trees. BEAUti also supports the
	    new *BEAST method.

	    Relaxed clock refinements: The uncorrelated relaxed clock models have
	    been refined by the addition of two new operators to address (valid)
	    criticisms levelled in "Bayesian estimation of species divergence times
	    from multiple loci using multiple calibrations", Rannala and Yang (2007).
	    The change allows more than one branch to have the same relaxed clock
	    rate category. In practice this will only have any appreciable impact on
	    trees that have a small number of branches (< 15 taxa).

	Bug Fixes
		Many bugs fixed that were introduced in 1.5.0 including:
		
		Issue 38: If partitions are unlinked then the base frequencies should be 
	              calculated from each partition separately;
		Issue 80: ant build generates a broken beast;
		Issue 81: ant build release fails after recent changes to beauti;
		Issue 82: dr.app.util.Utils is broken (use of java 1.6 features?);
		Issue 97: Remove "Link All/Unlink All" buttons from Data Tab;
		Issue 98: Request to be able to view data partition alignments;
		Issue 99: Suggestion: Clock Models tab;
		Issue 100: Request to revise UI of "Choose Fix Rate Option";
		Issue 103: Comments and suggestions for "MCMC Tab";
		Issue 106: Single locus but multiple codon partitions: Doesn't allow 
		           'Fixed mean rate';
		Issue 109: BEAUti: Generating XML - no file overwriting warning?;
		Issue 110: BEAUTi: excludedTaxonSetsComboBox and includedTaxonSetsComboBox 
		           in Taxon Sets panel not updating
		Issue 114: Beauti Priors panel for starbeast;
		Issue 115: Beauti starbeast: missing updown operator for first gene;
		Issue 116: Make TN93 available in BEAUTi;
		Issue 118: Beauti defaults - clock.rate in starbeast;
		Issue 119: Beauti fails;
		Issue 120: Beauti silliness - warn about not saving when nothing was done;
		Issue 121: Beauti generates spurios multiple upDown operators;
		Issue 124: Create method to check calibration situation;
		Issue 125: Tree prior panel affecting isShareSameTreePrior check box wrongly.
		        
		All issues can be viewed at http://code.google.com/p/beast-mcmc/issues/list

================================================================================

Version 1.5.0 released 4th August 2009
	This was a major new version with numerous new features and many bugs -
	see release 1.5.1 for details.
	
	Bug Fixes
		Many new bugs were introduced. 
	
================================================================================	

Version 1.4.8 released 27th July 2008
	New Features:
		A birth-death model of speciation. This is the model of Tanja Gernhard 
		(The conditioned reconstructed process, J Theor Biol, 2008).
		
		There is now an option to dynamically rescale the likelihoods of trees 
		to avoid loss of precision. This can avoid problems with large trees 
		but may affect performance. See on-line documentation for details.

	Bug Fixes:
		Improvements to how uncorrelated relaxed clocks are sampled. This will 
		be an improvement more for small trees than large.
		
		Fixed a problem setting the number of groups for the Bayesian Skyline 
		Plot in BEAUti.
		
		A warning message is given if a speciation process is selected for 
		serially-sampled sequences.

		LogCombiner ignores lines starting with a '#' as a comment line.
		
		Trees are written with a standard (alphabetical) ordering of taxa to 
		allow them to be read by AWTY.
		
		For writing NEXUS tree files, taxon names with illegal characters (such 
		as spaces or semicolons) are now quoted.
		
		LogCombiner now uses the '.' as the decimal separator irrespective of
		country or language. This is to standardize with other programs.
		
Version 1.4.7 released 1st February 2008
	New Features:
		BEAUti can now set nucleotide frequencies to be sampled or equal as well 
		as the empirically estimated (the previous default).
		
		Individual operators can now be turned on and off in BEAUti (for example
		to sample on a fixed tree topology).

	Bug Fixes:
		BEAST now generates starting trees with certain taxon constraints that 
		caused problems before.
		
		Some numerical problems with the Expansion and Logistic models have been
		fixed or at least improved for certain situations.
	
		Fixed a problem in which BEAUti's Prior Distribution dialog was freezing
		when a very large lognormal mean was set.
		
		A seed of zero crashed BEAST - seeds must be > 0 now.
		
		The command-line version of TreeAnnotator wasn't accepting a target tree
		file name.
		
		Fixed a problem in LogCombiner where if the Run button was pressed 
		before the user had finished editing a burnin the value was ignored.
		
		Fixed an issue with BEAUti running under Mac OS X 10.5 (Leopard) where 
		the text box for the substitution rate was tiny.

Version 1.4.6 released 26th September 2007
	Bug Fixes:
		Fixed a problem in which the lognormal distribution wasn't giving the
		required distribution as prior.
		
		Fixed a problem with TreeAnnotator not completing when finding the 
		Maximum Clade Credibility tree.

Version 1.4.5 released 31st July 2007
	Bug Fixes
		Some monophyletic constraints defined in BEAUti failed to run in BEAST.
		
		The priors table didn't update when the tree prior was changed.

Version 1.4.4 released 12th July 2007
	New Features:
		Improved speed of relaxed clock by more judicious updating of the 
		likelihood when rates change on a few branches.
		
		Slight improvement in speed calculating the coalescent prior.
		
		The taxa and translate lists in NEXUS trees files can now be sorted
		alphabetically (and this is the default in BEAUti). This will help
		comparisons of trees files using certain software that assume taxon
		orders are the same (namely AWTY).
		
	Bug Fixes
		Log normal prior element required meanInRealSpace attribute which
		prevented older XML file from running without modification. This 
		attribute is now optional.

Version 1.4.3 released 18th June 2007
	Bug Fixes
		The Yule tree prior was wrongly implemented.

		BEAUti did not allow some types of compatable monophyly 
		constraints.
		
		BEAST did not always simulate starting trees with enforced
		monophyly correctly.
		
		BEAST ignored specified offsets for exponential priors on 
		parameters.
		
		BEAUti ignored user specified offsets for gamma distribution 
		priors on parameters.

Version 1.4.2 released 25th April 2007
	New Features:
		Taxon sets can now have monophyly enforced using BEAUti.

		Starting tree is now compatible with monophyly constraints
		and uniform priors on tMRCAs.

		Relaxed clock statistics (meanRate, etc.) are now in the priors
		table.

	Bug Fixes
		Fixed problem with rate estimation under the 2 partition codon
		specific rates models (including SRD06).

		Fixed problem setting Bayesian Skyline group count in BEAUti.

Version 1.4.1 released 25th January 2007
	Bug Fixes:
		BEAUti did not accept the number of skyline groups properly.
		
		BEAUti was not able to 'guess dates' using a specified prefix.
		
		Fixed a problem using exponential distribution as priors.
		
		LogCombiner could mix up taxon labels when combining multiple 
		tree files. This problem would not affect the reconstruction of
		skyline plots.
		
Version 1.4 released 31th October 2006
	New Features:
		Faster likelihood calculations after rejecting a state. Whilst 
		the improvement in speed will vary, the indications are that
		this is a significant overall speed improvement.
				
		Rates for relaxed clock models can be written embedded in the 
		tree for later analysis.
		
		2 new accessory programs: LogCombiner for combining multiple 
		runs into single log files and TreeAnnotator which annotates a
		given target tree with posterior estimates from a BEAST sample
		of trees.
		
		BEAUti can now create TaxonSets and apply prior probability 
		distributions to the tMRCA of these.
		
		BEAUti can now save and load "Template Files" containing model
		settings but not data.
		
		BEAUti can be run non-interactively as a command-line using the 
		template files.
	
		The order of parameters logged in BEAST files created by BEAUti 
		has been changed to make it easier to compare files with different
		models in Tracer.

	Bug Fixes:
		BEAUti did not use the specified fixed substitution rate.

		Fixed a problem using UPGMA as an initial tree - would sometimes
		give ? in log files instead of posteriors.

		Fixed a problem with BEAUti not loading data when using a non-
		english operating system.

		Fixed a problem using gamma distribution as priors.

Version 1.3 released 30th August 2005
	New Features:
		"Relaxed Clock" models.
		New prior selection for parameters using BEAUti.

	Bug Fixes:
		Problem with distributionLikelihood including all data twice
		resulting in the distributions being too tight.

		Improved error reporting.

Version 1.2 released 24th February 2005
	New Features:
		"Bayesian Skyline" demographic model.
		Logistic demographic model.

Version 1.1.2 released 27th August 2004
	Bug Fixes:
		Amino Acid models were not being set correctly
		resulting in the use of an equal-rates model.

Version 1.1.1 released 24th August 2004
	New Features:
		Can now switch autoOptimize on or off for individual 
		operators. This overrides the setting for the <mcmc>
		element.
		
		Default weights for certain operators have been changed 
		in BEAUti to improve performance.
		
	Bug Fixes:
		Fixed a bug in BEAUti in which unlinked codon analyses
		produced non-working XML files.

		Fixed a bug where BEAST wouldn't run certain old XML files
		throwing a null-pointer exception when writing a log file.

		Doesn't stop with RuntimeException when a state is proposed
		that has a really bad (underflowing) likelihood.

Version 1.1 released 5th August 2004
	New Features:
		An auto-optimize function that removes the need to 
		perform manual tuning of operators.
		
		Improvement in speed of likelihood calculations for
		nucleotides.  
		
		Now includes BEAUTi as part of the BEAST package. In 
		future these will be distributed together with matching
		version numbers.
		
	Bug Fixes:
		Various minor problems with parsing XML have been fixed

Version 1.0.3 released 12 July 2003
	New Features:
		Improved tree log analyser. Now gives mean node heights 
		(branch lengths) on trees with a frequency > 100.

	Bug Fixes:
		Various minor problems with parsing XML have been fixed

Version 1.0.2 released 27 June 2003
	New Features:
		Improved tree log analyser. Now gives mean node heights 
		(branch lengths) on trees with a frequency > 100.

	Bug Fixes:
		Fixed the wrong coalescent likelihood function introduced 
		in the last version.

		Various minor problems with parsing XML have been fixed
		(including GTR model, NormalDistribution and others).

Version 1.0.1 released 23 June 2003
	This version introduced a 'fix' for the coalescent likelihood 
	function which turned out to be erroneous. This version should 
	not be used.

Version 1.0 released 10 June 2003
	First released version.