DO NOT USE -- FOR TESTING PURPOSES ONLY.
Very early preliminary release for Linux only with Java 8 included.
Fix auto-set clock rate in BEAUti when independent trees are involved
Loading two dimensional data into trait dialog robustified
Make NexusParser more robust and allow Fasta imports to select from all data types
Fix TreeAnnotator -heights processing issue
Make Prior.sample() obey parameter bounds
Fix TipDateRandomWalker to ensure heights are always >= 0
Remove superfluous new lines in XML produced by BEAUti
SimulatedAlignment correctly links indices of tree to alignment
Option 'ascii' added to Logger to allow it to convert output to ascii or not
Add upper limit to delta exchange optimization
Made tree input to RatesStatistic required to ensure appropriate behaviour
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
Patch release that fixes output bug introduced in the GUI version of LogCombiner in v2.6.4.
To install, first install v2.6.4, then upgrade using the package manager, or by starting BEAUti, which automatically checks for updates.
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
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
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
- 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
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.
- 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