                    BEAST v2.6.6 2021
                 Beast 2 development team 2011-2021
Version History
Last updated: August 2021

All issues can be viewed at https://github.com/CompEvol/beast2/issues
================================================================================
Version 2.6.6
	Fix so that when not using ambiguities, the nucleotide 'U' base pair is correctly interpreted
	Fix tree annotator for lower bound on common ancestor heights
	Make the -prefix option work when not using a directory
	Allow '=' signs in options passsed with -D
	Add filter input to SwapOperator
	Fix so DocMaker works again
	Update for R script to create EBSP plots
	Limit size of Trie to prevent memory leaks for some models
	More robust Nexus parser
	Improved error messages

Version 2.6.5
	The GUI version of logcombiner produces output again

Version 2.6.4
	Applauncher picks up BEAGLE
	Less clutter on screen output
	Bayesian skyline plot has a proper prior alternative for the first element of the popSizes parameter
	Fix DensiTree launcher for Windows
	LogCombiner can now write to stdout
	FilteredAlignment can deal with missing and ambiguous values
	Node now recognises age trait
	Allow packages to be released in github release area again
	Add differentRandomIndex to UpDownOperator
	Checksum support for developers chasing incorrectly calculated likelihoods

Version 2.6.3
	Robustify resume
	RandomTree deals with calibrations in date-forward mode
	BEAST new `-DF` and `-DFout` options
	Default values for user defined values
	LogAnalyser new `-tag` option
	Let `Input.setValue()` ignore empty lists (instead of throwing exception) 
	User data type lengths are not required to be equal any more
	Robustify RPN calculator

Version 2.6.2
	Allow operator schedule changes in BEAUti
	Fix quantile parameterisation of relaxed clocks
	Add batch file for Windows command line usage
	Improve error messages
	Provide better access in API for developers

Version 2.6.1
	Fix bug in BEAUti so that template of "last" package is recognised
	Make loganalyser deal with spacees in trace log names
	Add column to LogAnalyser -oneline output
	Random local clock fix for unscaled rates

Version 2.6.0
	Robustify application launching and package upgrading (especially for Windows)
	Make sequenceSimulator less sensitive to taxa ordering
	Improved error messages
	XML being produced is more standardised

BEAUti
	Make help menu extendible to add for example automatic methods section generator        
	Saves last accessed directory between sessions
	Default bounds on BSP pop sizes and random local clock rates updated
	Let GuessPatternDialog handle empty fields.
	Adding MRCAPriors more robust when multiple alignments share a tree
	More complete Nexus parser

For developers
	More flexible options for constructing BEAST objects 
	More access methods to core classes
    	Added BEASTInterface::notClonable

Version 2.5.2
	More robust release for Windows that includes JRE
	Fix AppLauncher for OS X
	Robustify start scripts for OS X, Linux
	Implement rate parameterisation for uncorrelated relaxed clock model
	Improved error messages	
	Relaxed API giving more access to package developers
	Node.getMetaData() now returns null on key not found
	Pass -Xss arguments through launchers to set stack size
	DOIs point to preferred resolver
	Fix multi-threading issue with parameteric distributions
	Remove posterior ESS from screen log

Version 2.5.1
	Add -X flag to all applications, so more memory can be allocated
	Fix some OS X with Java 9+ anomalies
	More robust OS X CUDA check
	More robust launch scripts
	Better error reporting
	More robust package manager
	TreeAnnotator handles taxa that are numbers now
	Allow multiple -D arguments to BEAST, allows commas in user defined variables	

Version 2.5.0
        BEAST & friends are now compatible with Java 8, 9 and 10.
        All appllications start a bit faster now package discovery is cached.
        Versions available with Java bundled
        
BEAST   
        A command line option is added to parameterise XML files.
        Maximum MCMC length was 2147483647 is now 9223372036854775807.
        Fix for resume of coalescent, which sometimes failed.
        RPNCalculator logs starting from 1 consistent with multi dimensional parameters

BEAUti
        Facility to automatic update packages when BEAUti is started
        Tip dates panel supports wider range of formats
        Added clear classpath menu 
        More robust NEXUS parsing
        Allow top level templates, to easily switch between say MCMC and nested sampling
        Bug fix for unlimited prior distributions to be changed
        More robust substitution model initialisation
        
Utilities: 
        Renamed appstore => applauncher to preven confusion with OS X app store.
        Renamed addonmanager => packagemanager 
        Packagemanager has an -update option to check for updates and -updatenow to install without asking
        Better progress reporting on logcombiner, treeannotator, loganalyser


Version 2.4.8 January 2018
BEAST   Ensure BeagleTreeLikelihood gives correct likelihood with RNA data.

Version 2.4.7 July 2017
BEAUti
	Relabel buttons: "Guess" is now "Auto configure" in tip dates panel. "+" button on priors panel is now "+ Add Prior".
	More sensible default date value for taxa without date specified in tip dates panel.
	Make sure the appropriate tree is used in MRCAprior.
	Make sure tips with 'fixed' distributions imported from Nexus do not get estimated.
	Robustify NEXUS parser.
	Taxa could be duplicated in taxon list in NexusParser.
	Prevent accidentally cloning of up-down-all operator in StarBeast.
	
BEAST
	Default locale set to English so full stops are used in NEXUS output.
 	Warn if Yule (or BD) conditions on root, but no root MRCAPrior is set.
	Robustify resume 
	Suppress "Overwrite (Y/N)?" message when BEAST runs in console.
	Stop chain when encountering a +infinity posterior.
	Check that taxon set is specified when using RandomTree.
	Normalise stateNodes so XML characters ('"&<>) get escaped properly when writing state files.


Appstore
	Improved formatting of app list.

TreeAnnotator 
	Now adds common ancestor height estimates as attributes.

API updates:
	Changed access levels of a few methods in nexus parser.
	Add Tree scale and ScaleOperator test.
	Add new Tree constructor from root node.
	Add support for input/output of non-binary trees.
	Add Input.set() method.
	BeautiAlignmentProvider getAlignments method added to facilitate scripting.
	TreeParser correctly parses tree edge length metadata, and improved error reporting.

Version 2.4.6 May 2017
    BEAUti
	    Starting trees can now be edited (default random, choice of cluster and newick trees)
	    Allow alignments to be replaced, so old analyses can be used for new data
		Fix fasta file import bug that marked sequences as amino acid while it should be nucleotide
	    Keep trees linked when splitting alignment on codon positions
	    Automatically set estimate flag on shape when choosing rate categories
	    Fix display of integer alignments

    BEAST
    	Better documentation
    	More robust XMLParser
	    Prevent double counting of offset in ParametricDistribution.sample
	    
	DensiTree version updated to v2.2.6
	
Version 2.4.5 January 2017

	BEAUti
		Clone fix that deals with edited priors
		Package manager can now install specific package versions, not only the latest
		Improved data type guessing on importing FASTA files
		Log MRCAPriors imported through NEXUS files
		
	BEAST
		Added -strictversions flag to indicate only package versions specified in XML should be loaded.
		Tree parser fixes
		StarBeastStartState now takes bounds of parameters it sets in account
		Allow nested operator schedules
		Improved error reporting
		
	Package manager
		Added -version flag to specify exactly which package version to install.	
	
	TreeAnnotator
		Now calculates 2D HPDs by default (for phylogeography analyses)
		Added -nohpd2D flag to suppress 2D HPD calculation
		Added -noSA flag to suppress tree set being seen as that of a sampled ancestor analysis


Version 2.4.4 November 2016
	Fix that prevented starting any BEAST application on Mac Sierra
	
	Smooth out some issues with importing Nexus files in BEAUti
	
	TreeAnnotator fix for use with user defined trees to annotate
	
	Allow smaller log files by logging fewer significant digits of metadata

Version 2.4.3 August 2016
	
	BEAUti
		Support for tip date sampling by setting 'tipsonly' in MRCA Priors
		Allow packages to specify priors, e.g. multi-monophyletic constraints in BEASTLabs
		Allow packages to specify file importers, which allows microsattelite support through the BEASTvntr package
		Gamma distribution allows multiple parameterisations
		Packages used now encoded in XML, for better error reporting of missing packages
		Better looking on high-res screens
		
	Package Manager
		Links to documentation available
		Better layout
		
	BEAST
		allow multiple citations per class
		allow trait sets with unspecified dates
		allow multiple arguments to Sum
		improved error reporting
		
	TreeAnnotator fix for phylogeography in low-mem mode.
	LogCombiner suppress duplicate '=' in tree output
	
Version 2.4.2 June 2016
     Applications are scalable, making them visible on high resolution screens

     BEAUti
         improved error reporting
     BEAST
         improved error reporting
         prevent closing window on parsing errors
     
     LogCombiner requires much less memory than before
     
     Densitree updated to version 2.2.5
     
Version 2.4.1 April 2016
     BEAUti
         import of calibrations from NEXUS files
         add App Launcher menu
         make missing *BEAST template available again
         save in old style XML, with less restricions on taxa names 
     Streamlined upgrades of BEAST
     
     BEAST
     	improved BEAGLE library loading from CLI
        test for spurious CUDA drivers on OSX, which used to cause a crash, but now provides instructions on how to solve this
        improved operator tuning for slightly better performance
        improved error reporting

     LogAnalyser shows progress on CLI again by default
        
Version 2.4.0 February 2016
    BEAST improved performance
        up to 2x faster when using proportion invariant sites
        improved threading support        
        "instances" flag replaces beagle_instances
        faster MRCAPrior handling
        StartBeastStartState works with calibrations with other than CalibratedYule
    
    BEAUti
        show mean of parametric distributions in priors panel
        better taxon management preventing adding numbers to taxon names 
        improved layout tip dates panel
        improved package list errors
        *BEAST clock cloning fix
        Allow setting branch length as substitution option on tree logger
        Improved JSON support
        
    Package manager
       Allow BEAST to be upgraded as a package
       Improved GUI
    
    For developers: http://beast2.org/2016/02/04/what-will-change-in-v2-4-0-for-developers/

Version 2.3.2 December 2015
	BEAUti
		path corrected so Standard and StarBeast templates are visible under templates menu
		import of traits from file when partitions are split fixed
		cloning of scripts with partition information fixed
		set up weights of FixedMeanRate operator when ascertainment correction is applied
		allows ParameterInputEditor to edit Parameter inputs
		
	BEAST
		add "-validate" command line option for parsing XML files without running them
		more efficient MRCAPrior
		more robust RandomTree
	
	LogCombiner
		ensured logcombiner burn in editing finished properly
		
	LogAnalyser now has one line per file mode, and CLI script added for ease of launch
		
	More sensible error messages (in TreeParser, RPNCalculator, NodeReheight, and more).

Version 2.3.1 September 2015
     BEAUti
       robustify (un)linking
	   improved Fasta import

	BEAST
	   support for uncertain alignments (see examples/testJukesCantorShortUncertain.xml) 
       improved error messages

    TreeAnnotator allows lower memory consumption

	AppStore, LogCombiners, LogAnalyser improved command line interface 

	Antlr based tree parsing

        DensiTree updated to v2.2.3

	BinaryCovarion model option to run as reversible model 

	Set log level by environment variable
	
Version 2.3.0 May 2015
	BEAUti fixes
		cloning, linking, unlinking bugs fixed
        more robust templates
        calibrations can be deleted now
		improved access to package folders
        improved import menu

	LogCombiner improved command line interface

	Fix synchronisation issues affecting ThreadedTreeLikelihood
    
	Auto load beast.jar, giving footprint for Mac

	Bug fix in EigenDecomposition affecting asymmetric rate matrices

	Reduced dependency on taxon order making multiple partition handling more robust

    Can keep running v2.2 and its packages alongside v2.3

	DensiTree updated to v2.2.2

Version 2.2.1 March 2015
	Support for multi-gamma-site-model package 

	BEAUti some bug fixes involved in linking/cloning + some cosmetic changes

	Better error reporting:
    - in BEAUti, estimate of relative substitution rate for single partition only caused BEAST to hang
    - check correct java version (8) is used
	- package manager warns when there is no internet connection

	Improved NEXUS Standard datatype support

	TreeAnnotator improved sampled ancestor support

	CLI script now sensitive to JAVA_HOME environment variable

	DensiTree updated to v2.2.1

Version 2.2.0 January 2015
	Uses Java 8 to facilitate package development, thus preventing version clashes with packages

	BEAUti default settings preventing common errors, template fixes, layout enhancements, error logging

	Enhanced package manager
	
	Better error reporting for finding common issues with XML files (such as *BEAST gene trees not covering all species)

	Improved install for Mac

	Over 300 commits for small bug fixes and performance enhancements (more readable XML, better NEXUS parsing, TreeAnnotator fix, etc.)

Version 2.1.3 May 2014
	Patch release
	
	*BEAST template fixed

	add AppStore for conveniently launching applications from packages

	improved FASTA support

	a few small fixes (BEAUti displays of log normal, monophyletic constraint logging, allow import of alignments with same name in BEAUti,etc.)


Version 2.1.2 April 2014
	Patch release

	BEAUti handles multiple partitions more conveniently

	improved package management

	fix bug in *BEAST template
	
	many small fixes (FASTA support, stochastic distributions, *BEAST operator weighting, etc.)


Version 2.1.1 January 2014
	Patch release speeding up BEAUti to handle large Nexus files and handle multiple files.


Version 2.1.0 December 2013
	Support for many more packages, including 
		o CladeAge for fossil calibrations
		o Sampled Ancestor Trees
		o Multi Type Trees for structured coalescent
		o Birth-Death SIR model
    If not already available these will be so soon.

	Support for JSON file format

	Beagle update issue resolved -- no more incorrectly calculated likelihoods

	Core refactored, for ease of developing packages

	*BEAST start state for getting faster through burn-in

	BEAUti many small fixes supporting more packages

	DensiTree and TreeAnnotator updated



Version 2.0.2 February 2013

	Beagle scale issue resolved, resulting in potentially faster 
	treelikelihood calculations

	Treeannotator and logcombiner updated to version 2
	
	BEAUti - use-ambiguities flag in partition panel

	colt and apache math-commons libraries included so not all add-ons
	need to supply them separately

	Support for path-sampling through beastii add-on



Version 2.0.c released on 1st December 2011

	New Features:
	
    Allows resuming an MCMC chain. Handy when the chain turns out to
    converge slower than expected.

    Real time tracking of ESSs while running a chain.

    Beauti allows reloading files, so that small changes do not require any
    XML editing.

    For developers, code is better documented, and only the most relevant
    classes are part of Beast 2 (i.e. no experimental research code), making
    it easier to learn.

    Easily extendible: for example, the BeastII add-on supports multi chain
    MCMC, some experimental likelihood calculations that are potentially
    faster than the base implementation, and a spread sheet GUI for
    manipulating models.    
