BEAST 2.4.5

@rbouckaert rbouckaert released this Feb 1, 2017 · 9 commits to master since this release

   BEAUti
            Clone fix that deals with edited priors
            Package manager can now install specific package versions, not only the latest
            Improved data type guessing on importing FASTA files
            Log MRCAPriors imported through NEXUS files
            
    BEAST
            Added -strictversions flag to indicate only package versions specified in XML should be loaded.
            Tree parser fixes
            StarBeastStartState now takes bounds of parameters it sets in account
            Allow nested operator schedules
            Improved error reporting
            
    Package manager
            Added -version flag to specify exactly which package version to install.        
    
    TreeAnnotator
            Now calculates 2D HPDs by default (for phylogeography analyses)
            Added -nohpd2D flag to suppress 2D HPD calculation
            Added -noSA flag to suppress tree set being seen as that of a sampled ancestor analysis

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BEAST 2.4.4

@rbouckaert rbouckaert released this Nov 7, 2016 · 62 commits to master since this release

Fix that prevented starting any BEAST application on Mac Sierra

Smooth out some issues with importing Nexus files in BEAUti

TreeAnnotator fix for use with user defined trees to annotate

Allow smaller log files by logging fewer significant digits of metadata

More details here.

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BEAST 2.4.3

@rbouckaert rbouckaert released this Aug 16, 2016 · 93 commits to master since this release

BEAUti
    Support for tip date sampling by setting 'tipsonly' in MRCA Priors
    Allow packages to specify priors, e.g. multi-monophyletic constraints in BEASTLabs, geographical priors in GEO_SPHERE
    Allow packages to specify file importers, which allows microsattelite support through the BEASTvntr package
    Gamma distribution allows multiple parameterisations
    Packages used now encoded in XML, for better error reporting of missing packages
    Better looking on high-res screens

Package Manager
    Links to documentation available
    Better layout

BEAST
    allow multiple citations per class
    allow trait sets with unspecified dates
    allow multiple arguments to Sum
    improved error reporting

TreeAnnotator fix for phylogepgraphy in low-mem mode.
LogCombiner suppress duplicate '=' in tree output

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BEAST 2.4.2

@rbouckaert rbouckaert released this Jun 22, 2016 · 144 commits to master since this release

 Applications can be scaled, making them visible on high resolution screens

 BEAUti
     improved error reporting
 BEAST
     improved error reporting
     prevent closing window on parsing errors

 LogCombiner requires much less memory than before

 DensiTree updated to version 2.2.5

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BEAST 2.4.1

@rbouckaert rbouckaert released this Apr 25, 2016 · 181 commits to master since this release

BEAUti

  •     import of calibrations from NEXUS files
    
  •     add App Launcher menu
    
  •     make missing *BEAST template available again
    
  •     save in old style XML, with less restricions on taxa names 
    
  • Streamlined upgrades of BEAST
    

BEAST

  •    improved BEAGLE library loading from CLI
    
  •    test for spurious CUDA drivers on OSX, which used to cause a crash, but now provides instructions on how to solve this
    
  •    improved operator tuning for slightly better performance
    
  •    improved error reporting
    

LogAnalyser shows progress on CLI again by default

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