BEAST v2.6.4 release

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 & Mac
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

BEAST v2.6.3 release

    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

BEAST v2.6.2 release

    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

BEAST v2.6.1 release

• Fixes bug in BEAUti so that template of "last" package is recognised
• Makes loganalyser deal with spacees in trace log names
• Adds column to LogAnalyser -oneline output
• Has random local clock fix for unscaled rates

More details are available here:
http://www.beast2.org/2019/08/08/what-is-new-in-v2.6.1.html

BEAST v2.6.0

Main changes

    Robustify application launching and package upgrading (especially for Windows)
    Faster BEAUti processing of large number of partitions

Other changes

    Make sequenceSimulator less sensitive to taxa ordering
    Improved error messages
    XML being produced is more standardised
    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

There are more details for users and developers on the beast2.org website.

BEAST 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

BEAST 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

BEAST 2.5.0

Note that if you use this, there may be packages that are still not available. If you need to use an unavailable package, you can use BEAST v2.4.8 instead.

BEAST 2.4.8

Ensure BeagleTreeLikelihood gives correct likelihood with RNA data.

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.