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Pre-release

DO NOT USE -- FOR TESTING PURPOSES ONLY.

Very early preliminary release for Linux only with Java 8 included.

4da8b9b
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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

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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
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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.

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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
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    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
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    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
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  • 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

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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.

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  • 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