Releases: CompEvol/beast2
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).
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!