BEAST 2.3.1 release

Note: requires Java 8.

    BEAUti fixes
       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

BEAST 2.3.0 release

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

BEAST 2.2.1 release

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

BEAST v2.2.0 release

NOTE: you need Java 8 to run BEAST (freely available from http://java.com/)

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.)

BEAST v2.1.3 release

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 and other distributions, monophyletic constraint logging, allow import of alignments with same name in BEAUti,etc.)

The beastEBSP.jar and beastEBSP.src.jar contain a fix for the EBSP analyser, which can be run standalone.

BEAST v2.2.0 pre-release

Pre-release, for the adventurous only...

BEAST v2.1.2 release

RELEASE 2.1.2 -- NOTE: the StarBeast template is broken-- do not use for *BEAST analysis

Patch release
o BEAUti handles multiple partitions more conveniently
o improved package management
o fix bug in *BEAST template
o many small fixes (FASTA support, stochastic distributions, *BEAST operator weighting, etc.)

BEAST v2.1.1 release

Patch release speeding up BEAUti to handle large Nexus files and handle multiple files.

BEAST v2.1.0 release

exactly as it was!

BEAST v2.0.2 release

make addon manager pick version dependent addons