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BEAST Changelog

What's new in BEAST 2.0.2

Apr 16, 2013
  • Beagle scale issue resolved, resulting in potentially faster treelikelihood calculations
  • Treeannotator and logcombiner updated to version 2
  • BEAUti - use-ambiguities flag in partition panel
  • Colt and apache math-commons libraries included so not all add-ons need to supply them separately
  • Support for path-sampling through beastii add-on

New in BEAST 2.0c (Mar 1, 2013)

  • New Features:
  • Allows resuming an MCMC chain. Handy when the chain turns out to converge slower than expected.
  • Real time tracking of ESSs while running a chain.
  • Beauti allows reloading files, so that small changes do not require any XML editing.
  • For developers, code is better documented, and only the most relevant classes are part of Beast 2 (i.e. no experimental research code), making it easier to learn.
  • Easily extendible: for example, the BeastII add-on supports multi chain MCMC, some experimental likelihood calculations that are potentially faster than the base implementation, and a spread sheet GUI for manipulating models.

New in BEAST 1.7.4 (Nov 19, 2012)

  • Critical Bug Fix:
  • Issue 664: Some priors are not being evaluated.
  • http://code.google.com/p/beast-mcmc/issues/detail?id=664
  • Bug Fixes:
  • Issue 661: Fails to generate XML after particular sequence of options.
  • Issue 660: For trait specification errors, error messages should include name of taxon.

New in BEAST 1.5.4 (Apr 6, 2010)

  • Bug Fixes
  • Many bugs fixed that were introduced in 1.5.3 including:
  • Commas put into years displayed in BEAUti
  • examples/testCoalescent.xml
  • mcmc.operators
  • BEAUTi: review all initial rates and root height calculations
  • Fix unstable JUnit test
  • Improper JUnit test code causes incorrect failure in Hudson
  • BEAUTi: operator subtreeSlide size should not be INF
  • BEASTParserDoc is unable to generate Wiki format
  • BEAUTi: The user should *always* be allowed to fix the rates if they want
  • BEAUti: prior distribution error message "find incorrect number format"
  • Typo in BEAUTi - Unable to overwrite exsting file
  • BEAUti: AlignmentGenerator cannot print sequence with long sites properly
  • BEAST: ComplexSubstitutionModelParser can only refer to SVS not ComplexSubstitutionModel
  • BEAUti: remove exponential in VariableDemographicModel from BEAUti
  • BEAUti: EBSP VariableDemographicModel popSize value = populationMean value and indicators value = 0
  • BEAUti: avoid comma generated in the numbers in the log

New in BEAST 1.5.3 (Dec 15, 2009)

  • New Features:
  • GUI versions of BEAST show a dialog box to set various options that are otherwise only available by command-line.
  • Bug Fixes:
  • Issue 55: MCMC Screen log doesn't currently work.
  • Issue 70: beauty and partition into codon positions
  • Issue 72: Beauti should hard limit GTR model parameters
  • Issue 122: Ctrl-A in Beauti -> Exception
  • Issue 127: BEAUTi prior panel, prior upper and lower does not show
  • INFINITY
  • Issue 128: BEAUTi: tree prior Logistic Growth is not available for
  • calibration
  • Issue 146: BEAUTi: binary COVARION model
  • Issue 169: Editing the file name stem in BEAUti causes the insertion
  • point to jump to the end
  • Issue 173: BEAUTi: partially link exception
  • Issue 181: BEAUTi: need enhancement to default behaviour when adding
  • additional alignment after unlinking all
  • Issue 193: Improved convergence diagnostic: compute effective size of
  • combined runs by concatenating the samples
  • Issue 194: BEAUTi: prior setting exception when changing value
  • Issue 199: Tracer shows only first log file entry when multiples
  • entries have the same name
  • Issue 201: Editing file name stem in MCMC panel causes insertion point
  • to jump to end
  • Issue 202: Build scripts producing JDK 1.6 classes so distribution fails
  • on machines with JDK 1.5
  • Issue 203: Launch4j bug affecting the link of NucleotideLikelihoodCore.dll
  • Issue 204: BEAUTi: tree prior Constant Size is not working for node calibration
  • Issue 205: Tittle information disappeared in the console using windows
  • paramter to run BEAST
  • Issue 209: pathogen dose not compile
  • Issue 211: BEAUTi: Amino Acid site model xml is wrong
  • Issue 212: BEAST Linux version: need chmod 755 *
  • Issue 215: Default memory allocations for Mac packaging are too small
  • Issue 216: Default memory allocations for Linux packaging are too small
  • Issue 217: Problems with the Mac OS X packaging
  • Issue 218: BeastMain options dialog giving error "Illegal entry value
  • must be between 1 and 21474863647"
  • Issue 220: The shell scripts to launch BEAST in command line can't cope
  • with spaces in the path.
  • Issue 221: Reweight the substitution model operators in BEAUti
  • Issue 222: Naming of 'treeLikelihood' when only 1 partition
  • Issue 223: Set the 'operator analysis' file name as an attribute in
  • MCMC element
  • Issue 225: TreePartitionCoalescent is not existing
  • Issue 226: The parsers in release_parsers.properties need to be updated
  • Issue 227: Fix BeastDoc to generate tag doc for BEAST users
  • Issue 229: Another failure of testing framework
  • Issue 231: Delay the start of the performance measurement until after
  • full evaluation
  • Issue 232: Mac (Windows?) version of BEAST closes console on error
  • Issue 234: Make the dreaded "The initial posterior is zero" error a bit
  • more friendly to debug
  • Issue 236: dr.evomodel.operators.TraitGibbsOperator is duplicated with
  • parsers in either release_parser.properties or BeastParser.java
  • Issue 237: BEAUTi: taxon set not handling multi-tree partition
  • Issue 238: Naming of 'patterns' when only 1 partition
  • Issue 240: BEAUTi: useAmbiguities of treeLikelihood should be default
  • as true for binay Covarion
  • Issue 242: BEAUTi: create a check box to choose useAmbiguities in
  • treeLikelihood for binary data
  • Issue 244: URGENT: Default prior review
  • Issue 247: BEAUTi: wrong XML in frequecies choosing EMPIRICAL binary
  • COVARION model
  • Issue 248: BEAUTi exception (*BEAST) when linking some same taxa for a
  • tree model by given different taxa in total
  • Issue 250: BEAUTi: wrong alignment blocks for multi-gene when choosing
  • "create empty alignment"
  • Issue 253: BEAUTi add a pop-up box to check the default priors when
  • click Generate BEAST file
  • Issue 254: BEAUTi generate XML button should be disable after all data
  • partition removed
  • Issue 255: Turn off parser WARNINGs by default for released version
  • Issue 256: BEAUTi: Add comment in XML "skyride.logPopSize is log unit
  • unlike other popSize"
  • Issue 257: BEAUTi: Binary data and multiple partitions does not generate
  • the siteModel correctly
  • Issue 259: BEAUTi: Mac OS MCMC panel problem
  • Issue 260: BEAUTi: correct English
  • Issue 261: Error parsing element with id null
  • Issue 262: wrong XML of testCataclysmCoalescent.xml
  • Issue 264: ImportException: Number format error for

New in BEAST 1.5.2a (Oct 19, 2009)

  • Issue 44: Recent change (svn commit 773) breaks Beauti
  • Issue 75: "Unlink substitution model across codon positions has no effect
  • Issue 77: BEAUti v1.5 produces decimal operator weights that don't work with
  • old BEAST
  • Issue 94: Improve the prefix of PartitionClockModelTreeModelLink
  • Issue 123: BEAUti uses a poor choice of name for re-linking partitions
  • Issue 131: BEAUTi: rewrite Parameter and Operator class by Builder pattern,
  • and all referring methods
  • Issue 134: TN93 parser problem
  • Issue 135: Laplace prior has not been implemented in PriorParsers, but
  • appearing in BEAUTi.
  • Issue 136: BEAUTi log screen should show actual name instead of Rate 1, 2, ....
  • Issue 139: ImportnaceNarrowExchange should be ImportanceNarrowExchange
  • Issue 140: more options for *beast
  • Issue 144: BEAUTi: "In use" in Operators panel cannot be changed for those
  • operators belonging to PartitionClockModelTreeModelLink
  • Issue 145: BEAUTi: implement frequencies for binary model in the same way as
  • for DNA data
  • Issue 147: BEAUTi: if no leaf nodes selected in Taxon Set panel, the
  • corresponding tmrca should not appear in Prior panel
  • Issue 148: BEAUTi: illegal entry error for Clock Model panel
  • Issue 151: BEAUti: MCMC tab numerical fields reset after GUI events
  • Issue 154: No Nucleotide Likelihood Core in java.library.path
  • Issue 155: Warning message " ... does not match stored object with same id
  • and tag name ..." confused user
  • Issue 156: LogNormal in prior panel in Beauti
  • Issue 157: LogNormal in Beauti: Exception occurred during event dispatching
  • Issue 158: We should have the Inverse Gamma distribution in Beauti
  • Issue 160: Ant build for Mac version release
  • Issue 163: BEAUTi: unlink trees if allow different taxa
  • Issue 164: TreeAnnotator v1.5.1 incorrectly labels tree [bug report AND fix
  • solution!]
  • Issue 165: BEAUTi: some priors parameters keep changing
  • Issue 168: GMRF 'Skyride' complains about 'Share same tree prior' even if only
  • one tree
  • Issue 172: BEAUti: shareSameTreePrior should be disabled when there is only 1
  • tree model