v2.7.7 release

Version 2.7.7 June 2024
	o Add CCD to the list of recommended packages for TreeAnnotator CompEvol/beast2#1138
	TreeAnnotator GUI to pick up correct topology setting method CompEvol/beast2#1143
	BEAST
	o allow launch through `java -jar launcher.jar` CompEvol/beast2#1151
	o make alignment a StateNode CompEvol/beast2#1150
	o make Randomizer thread aware for better replicability of threaded runs CompEvol/beast2#1141	
	o make the AdaptableOperatorSampler ignore zero weight operators CompEvol/beast2#1136
	BEAUti
	o robustify for drag/dropping alignments CompeVol/BeastFX/#72
	o enable importing of alignments in files with .txt extension CompeVol/BeastFX/#78
	o remove HTML error messages CompeVol/BeastFX/#65
	LogAnalyser 
	o check added to prevent out of bound exception CompeVol/BeastFX/#81
	o add threading option to loganalyser when running with the oneline option CompeVol/BeastFX/#80

Release v2.7.6

TreeAnnotator allows packages to define new methods for creating summary trees CompEvol/BeastFX#71
BEAST
o parameters restored correctly after dimension change #1130
o robustify AdaptableOperatorSampler #1129
o fix element wise update in BactrianUpDownOperator #1126
o robustify Input when setting String values #1125
o allow trees to be exported correctly up to 999999 taxa
o enable close button in top bar of BeastMain dialog CompEvol/BeastFX#26
BEAUti
o TipDatesRandomWalker picks up correct tree
o make sure there are no numbers in tree taxon label block #1112
o improved error messages #1121
o indicate current theme in menu CompEvol/BeastFX#67
PackageManager resizes properly CompEvol/BeastFX#73
Applauncher improved layout CompEvol/BeastFX#77
Logcombiner fix default type when selecting files CompEvol/BeastFX#74

BEAST v2.7.5 release

        BEAST
        o bounded transforms added
        o higher default heap sizes for Windows
        o fixed command line argument parsing problem
        o enable quiting BEAST on OS X with cmd-Q BeastFX

        BEAUti
        o make linking by combobox changes work in partition panel of BEAUti
        o make drag/drop work in FileListInputEditor
        o add warning when adding hyperpriors on parametric distribution parameters
        o fix MRCA prior editor using the wrong tree (useful for multi-species coalescent analyses)
        o make it possible for the MCMC analysis to be replaced by others
        o added command line options to import nucleotide and AA fasta files.
        o improve tool tips for PriorInputEditor
        o fix prior panel parametric distribution display
        o make BEAUti show coalescent based tree prior inputs
        o show input dialog in center of BEAUti when drag/dropping files in partitions panel
        o fasta importer allows choosing datatype other than nucleotide and aminoacid 
	o BEAUti package manager buttons and taxon set editor show correctly with bootstrap theme 
	o x-axis of graph for parametric distributions in prior panel scales better 
        o better error messages 
	o selected theme indicated in view menu 

        Logcombiner GUI selects appropriate file types in file selector by default

BEAST v2.7.4

    BEAST:
    o add commmand line option for setting package user directory
    o more robust -version_file handling
    o make beast script find BEAGLE easier on arm cpu
    o allow BEAGLE usage for irreversible models, and make BEAGLE rootFrequencies input aware
    o more robust AVMN operator, uncertain alignment 

    BEAUti:
    o fix bug that prevented BEAUti from saving files if directory was removed 
    o make sure tip date operator is added when tips-only for MRCA prior is set
    o add functionality for auto-configuring tip date
    o allow 'Cancel' to stop BEAUti from closing
    o make short-cut keys on OS-X use command key instead of control

    Package manager 
    o selects CBAN clone if the default is not available
    o add -dir option to switch user package directory

BEAST v2.7.3 release

    Allow all packages to be installed, not just a small subset
    Add support for various packages
    Add `-packagedir` and `-version_file` CLI options to BEAST, BEAUti
    Extend XML variable substitution to text nodes
    BEAUti: fix bugs in templates
    BEAUti more robust when reloading XML into BEAUti

BEAST.base 2.7.2

package release for BEAST.base 2.7.2. This can be installed through the beast2 package manager / beauti.

BEAST v2.7.1 release

Fix assorted launch issues on Windows, Mac and Linux
BEAST: 
o GUI version outputs log files in same directory as XML file 
o added option to specify version.xml files explicitly. 
BEAUti:    
o Fix some BEAUti tooltip glitches, and BEAUti icon in Windows
o Remove AquaFX theme.
o Fix splash screen for BEAUti
o Add theming to Alert
o More responsive refresh + do not loose list view selection
Logcombiner converted to JavaFX
Applauncher: deal with superfluous icon not found messages 
DocMaker functional again
EBSPanalyser converted to JavaFX
Clean up BEAST code and some BEAUti code
DensiTree update to v3.0.2, fixing a display bug on Apple Silicon
Update migration script for converting v2.6 packages to v2.7

BEAST v2.7.0

Main new features:

    BEAUti has had a facelift, allows dark mode
    BEAUti templates reorganised for better performance
    "Help me choose" buttons added to BEAUti for direct targeted help
    Faster MCMC convergence due to smarter operators
    DensiTree v3.0.0 included, which allows pairwise comparison of tree sets
    Uses latest version of libraries: java 17, javafx, commons math, etc.
    Code reorganised, BEAST split into two packages: BEAST.base and BEAST.app
    Module like treatment of BEAST packages to prevent package library clashes

Click here for more details

BEAST v2.6.7 release

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

BEAST v2.6.6 release

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