Beast2 Versions Save

DO NOT USE!

For testing purposes only

TreeAnnotator allows packages to define new methods for creating summary trees CompEvol/BeastFX#71 BEAST o parameters restored correctly after dimension change CompEvol/beast2#1130 o robustify AdaptableOperatorSampler CompEvol/beast2#1129 o fix element wise update in BactrianUpDownOperator CompEvol/beast2#1126 o robustify Input when setting String values CompEvol/beast2#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 CompEvol/beast2#1112 o improved error messages CompEvol/beast2#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
        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:
    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

FOR TESTING PURPOSES ONLY

    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

    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

DO NOT USE: FOR TESTING ONLY

    Allow all packages to be installed, not just a small subset
    Add suppor 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

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

DO NOT USE: FOR TESTING PURPOSES ONLY

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