BEAST 2.4.7

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.

BEAST 2.4.6

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

BEAST 2.4.5

   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

BEAST 2.4.4

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

More details here.

BEAST 2.4.3

BEAUti
    Support for tip date sampling by setting 'tipsonly' in MRCA Priors
    Allow packages to specify priors, e.g. multi-monophyletic constraints in BEASTLabs, geographical priors in GEO_SPHERE
    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 phylogepgraphy in low-mem mode.
LogCombiner suppress duplicate '=' in tree output

BEAST 2.4.2

 Applications can be scaled, 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

BEAST 2.4.1

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

BEAST 2.4.0

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/

BEAST 2.3.3 prerelease

BEAST 2.3.3 prerelease

BEAST 2.3.2 release

    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).