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BEAST Changelog

What's new in BEAST 1.10.5 Pre-release

Aug 7, 2019
  • Clean screen output

New in BEAST 1.10.4 (Nov 11, 2018)

  • BEAST v1.10.4 fixes a bug when trying specify a burnin on the command line version of LogCombiner. It also introduces two new command line options specific to BEAGLE v3.1 (-beagle_threading_off and -beagle_thread_count).

New in BEAST 1.10.2 (Oct 8, 2018)

  • BEAST v1.10.2 is a minor bug fix release.

New in BEAST 1.7.2 (Jul 12, 2012)

  • New Features:
  • Implement Pearson Correlation Statistic
  • Bug fixes:
  • Issue 609: BEAUti duplicate prefix issue for multi-partition
  • Issue 611: BEAUti misnames the rates log file for BSSVS
  • Issue 612: BEAUTi robust counting XML was not overriding the default
  • stripping of ambiguous sites.
  • Issue 614: Writing Newick user tree in BEAUti doesn't quote taxa with space in the name
  • Issue 615: Multivariate traits generation by BEAUti was broken in the 1.7.1 update
  • Issue 618: BEAUti errors in States panel
  • Issue 619: BEAUti bug: cannot select a defined taxon set in
  • "Apply to taxon set" at the Tip date sampling
  • Issue 620: BEAUti only allows taxon sets >1 taxa
  • Issue 621: r3896 and r4062 broke Skyride in BEAUti
  • Issue 622: BEAUti: the "big" updown operator is missing for BEAST when calibration
  • Issue 623: Logging multiple branch rate models in same tree log is broken
  • Issue 624: Check boxes in BEAUti States panel do not line up
  • Issue 625: BEAUti XML invalid for 1 codon-partitioned partition and any 2nd partition
  • Issue 627: Error renaming clock-group
  • Issue 629: BEAST doesn't appear to be using multithreading

New in BEAST 1.7.1 (Jul 12, 2012)

  • New Features:
  • TN93 added to BEAGLE BEAST interface
  • Added BEAGLE rescaling options to options dialog
  • Added BEAGLE rescaling frequency commandline option
  • Bug fixes:
  • Issue 571: TN93 substitution model
  • Issue 594: BEAUti 1.7 has a redundant and non-functional Sequence Error
  • Model popup menu in SiteModelPanel
  • Issue 595: BEAUti: Markov jump state reconstruction not pushed to XML
  • Issue 596: BEAGLE performance has been degraded by choice of default scaling option
  • Issue 597: Use of -beagle_instances is broken in BEAST 1.7
  • Issue 598: BEAUti prior plot crashes given offset
  • Issue 599: Robust counting of dN/dS was producing incorrect XML
  • Issue 600: Truncation of prior distribution not interoperating with offset prior distribution
  • Issue 601: Markov Jumps counting of state changes wasn't generating correct XML
  • Issue 602: BEAUti prior dialog crashes if choose Laplace
  • Issue 603: BEAUti prior dialog not validate truncation and uniform bound and offset
  • Issue 604: RealNumberField FocusListener in prior dialog makes many popups
  • Issue 605: BEAUti complains about missing values in traits files

New in BEAST 1.7.0 (Jul 12, 2012)

  • New Features:
  • New Birth-Death speciation and epidemiological tree models. See citation panel in BEAUti for references.
  • Multivatiate continuous trait evolution models including Brownian motion and Relaxed Random Walk models.
  • Revamped Traits panel with more options for creating and editing traits.
  • New 'Create Partition from Trait' button to create a new data partition from an imported discrete or continuous trait.
  • New 'States' panel in BEAUti for ancestral reconstruction and sequence error model options for any data partition.
  • Robust counting models to reconstruct number of substitutions (including synonymous/non-synonymous for coding sequences).
  • Handling microsatellite data in BEAUti.
  • Clock group table in BEAUti to specify shared molecular clocks, and to distinguish with clocks applied to microsatellite data.
  • Construct Phylogenetic Hierarchical models in Priors panel of BEAUti.
  • More 'Guess Dates' options for parsing dates from tip labels. Includes parsing calendar dates.
  • More prior probability options for parameters and updated prior dialog box.
  • Species tree calibration for *BEAST in BEAUti.
  • Added Metropolis-coupled "BEAST MC3" into BEAST release.
  • Bug fixes:
  • Issue 43: treeTraceAnalysis fails due to comment in newick importer
  • Issue 51: log-normal prior in beauti not that usefull presentation
  • Issue 85: Add search filter above Included and Excluded taxa in Taxon
  • Sets panel of BEAUti
  • Issue 86: Missing validation in BayesianSkylineLikelihoodParser
  • Issue 88: LogCombiner should not allow thinning that is not compatible
  • with the original sampling rate
  • Issue 189: Gamma quantile fails on values close to 0 or 1
  • Issue 228: LogCombiner mishandles trees with attributes
  • Issue 312: BEAST continues to run (inappropriately) when sequence contains
  • invalid character
  • Issue 397: *BEAST in BEAUti is broken
  • Issue 398: BEAUti text message overlaps with button
  • Issue 399: Binary for TreeStat packaged with BEAST v1.6 has wrong version
  • number and icon
  • Issue 403: Starting tree generated with constraints by BEAUti is not correct
  • XML for BEAST
  • Issue 404: Make "Median heights" as the default of nodeHeightsCombo
  • Issue 405: RandomWalkOperator with reflecting boundary can grind to a halt
  • Issue 407: *BEAST needs to log species tree in { }, otherwise TreeAnnotator
  • keeps coming up with null exception on species tree
  • Issue 408: TreeAnnotator crashes with Null Pointer Exception on malformed
  • metacomment
  • Issue 409: BEAUti should explicitly generate uniform priors
  • Issue 410: "Improper priors" on posterior statistics
  • Issue 411: Incorrect validation and error message for random local clock
  • in BEAUti
  • Issue 412: BEAUti generates randomWalkOperator instead of
  • randomWalkIntegerOperator for branchRates.categories
  • Issue 413: BEAUti: duplicate class PartitionModelOptions causes model
  • link conflict
  • Issue 414: BEAUti: incorrect xml for multi-alignment when given complex
  • combination of clock model and tree model
  • Issue 416: Laplace prior parser should use scale same as BEAUti
  • Issue 417: BEAUti growthRate related XML causes -INF likelihood
  • Issue 418: Set maximun fraction digits for numbers displayed in BEAUti
  • prior panel
  • Issue 419: BEAUti RealNumberField should not throw Exception all the time
  • Issue 420: Add error message : Partitions cannot have the same name
  • Issue 422: BEAUti: add validation to check whether modified prior
  • initial value is between the boundary
  • Issue 423: delta exchange operator discription is wrong
  • Issue 425: BEAUti can't re-link subst models anymore
  • Issue 426: BEAUti does not preserve model settings when re-linking
  • Issue 427: BEAUti generates a mergePatterns even when it is enclosing
  • a single patterns element
  • Issue 429: Specifying more than 2 -temperatures on the command line
  • fails in parsing arguments
  • Issue 432: More detail for error message: *BEAST special part
  • generation has failed.
  • Issue 433: Typo in BEAUTi and example files
  • Issue 434: BEAUti: Initial value missing from prior dialog
  • Issue 435: UniformIntegerOperator did not include upper in the value
  • Issue 438: BEAST should tell you what frequencies belong to which
  • partition
  • Issue 442: BEAUti: taxon set table does not refresh after changing
  • tree model
  • Issue 443: BEAUti: change alpha default prior into Exponential
  • mean=0.5 offset=0.0
  • Issue 444: BEAUti: model table select row not update
  • Issue 445: BEAUti: clock rate configuration is not consistent
  • between clock model panel and prior panel
  • Issue 446: no indication that Checkboxes and rate text boxes are not
  • editable in Clock Group table
  • Issue 447: The Birth-Death models in the Trees Panel show a
  • citation - other models do not
  • Issue 448: Cannot load 2 nexus files with the same name
  • Issue 451: BEAST suggests using a non-integer for randomWalkIntegerOperator
  • Issue 457: BEAST should raise an error if binary dataType set but data is
  • not binary
  • Issue 466: Cannot run beauti / beast from git-svn clone
  • Issue 467: Native support for likelihoods is broken in linux
  • Issue 469: BEAUTi Covarion generation fails to add hfrequencies to operators.
  • Issue 477: Unable to calibrate species tree in BEAUti under *BEAST
  • Issue 481: Improve reporting of XML errors
  • Issue 493: Beauti does not show ploidy type for EBSP
  • Issue 499: Strip out should be false in the patterns when using binary
  • Covarion Model
  • Issue 500: remove RandomWalkIntegerOperator operator from relaxed clocks xml
  • Issue 501: Random Local Clock model has a bug when using multi-tree-likelihood
  • Issue 502: BEAUti prior panel: the lognormal prior chart cannot accept
  • negative numbers for M=log(mean), but it should
  • Issue 503: BEAUti operator analysis should be chosen as default
  • Issue 505: BEAUti Taxon Sets panel should have species rather than taxa
  • for *BEAST
  • Issue 506: The gamma prior is not reverted to what it was previously if
  • BEAST in unselected.
  • Issue 513: *BEAST constraint of the 'species' trait
  • Issue 522: BEAUti Taxon Sets panel should not allow to add taxon if no data
  • Issue 523: BEAUti Traits panel buttons enable/disable should adapt to data
  • and traits
  • Issue 527: change bound of Uniform prior into Double MAX or MIN
  • Issue 528: the BEAST parser for UniformPrior should throw a parser exception
  • if you attempt to give a bound at infinity.
  • Issue 529: proper priors to determine calibration in BEAUti
  • Issue 532: compileNativeLinux.sh uses non-optimal / fixed compile settings
  • Issue 533: Taxon set validation fires twice
  • Issue 535: SpeciesTreesPanel are not necessary
  • Issue 537: Robust counting code generation not producing good XML
  • Issue 538: move tree prior panel to the right of table
  • Issue 540: MCMC chain limited to 2^31-1 (Integer.MAX_VALUE)
  • Issue 541: BEAUti generates wrong xml when enforcing a uniform prior on
  • node ages
  • Issue 545: BEAUti taxon set compatibility should be focused on each tree
  • Issue 548: Beauti does not generate functional xml for msat data analysis
  • Issue 549: BeautiOptions.updateAll() stop user to customize clock rates
  • Issue 557: Removing a partition doesn't remove its unique taxa
  • Issue 560: wrong dependency to dr.evomodel.newtreelikelihood.
  • TreeLikelihood
  • Issue 562: BEAUTi : Birth Death Epidemiology Model update
  • Issue 565: hasIdenticalTaxa(List partitionDataList)
  • gives wrong boolean
  • Issue 568: same pattern id given to two different partitions
  • Issue 569: BirthDeathEpidemiologyModel bug
  • Issue 570: bug of unique attribute in pattern lists
  • Issue 572: BEAUti tmrca gives wrong prefix
  • Issue 573: BEAUti taxon set panel taxon set table incorrectly auto
  • selection
  • Issue 575: BEUAti should check for '--' in generated XML comments.
  • Issue 576: BEAUti calibrated Yule validation is missing one logic
  • Issue 577: BEAUti generator for *BEAST + calibrated Yule is broken
  • Issue 578: Add BEAST MC3 dialog and make it available in BEAST release
  • package
  • Issue 579: BEAUti : empty species set is created in *BEAST
  • Issue 580: BEAUti *BEAST did not check the empty species value
  • Issue 581: BEAUti prior dialog cannot accept 0 for typing 0.???
  • Issue 582: BEAUti Species Set cannot revert back to Taxon Set if
  • uncheck *BEAST
  • Issue 584: BEAUti prior dialog validation bugs
  • Issue 585: BEAUti keep getting "No leaf nodes selected" error message
  • Issue 586: BEAUti prior dialog Cancel not working
  • Issue 587: BEAUti prior dialog ignores validation in the text field if
  • pressing Enter key
  • Issue 588: Validation not working properly for PriorDialog
  • Issue 589: BEAUti lost Uniform bound validation
  • Issue 590: BEAUti prior dialog GUI logic bug
  • Issue 591: BEAUti prior dialog Truncated fields do not have correct
  • validation regarding parameter bounds
  • Issue 592: BEAUti tmrca name is not updated in prior panel if changing
  • its name in taxon set panel
  • Issue 593: TruncatedDistribution throw UnsupportedOperationException
  • for mean and variance

New in BEAST 1.6.2 (Jul 12, 2012)

  • New Features:
  • adds a "Beta Diversity" statistic to TreeStat program. This statistic takes a tree of two sets of species and computes the percentage of
  • the tree length shared by the two taxa sets allows BEAUti 'Guess Dates' dialog to parse out calendar dates from the taxon names
  • Updates all native nucleotide likelihood core files into 64 bit
  • For 32 bit machines, the user needs to rename the 32 bit files e.g. for Windows, rename NucleotideLikelihoodCore32.dll into NucleotideLikelihoodCore.dll) to replace the current 64 bit files
  • Bug fixes:
  • Issue 423: delta exchange operator description is wrong
  • Issue 424: TraitGuesser not extracting match within brackets (braces)
  • Issue 434: BEAUti: Initial value missing from prior dialog
  • Issue 435: UniformIntegerOperator did not include upper in the value
  • Issue 454: BEAUti: all the taxon sets are deleted when link/unlink tree
  • Issue 460: LogCombiner uses localized decimal point when writing trees
  • Issue 464: Localized decimal indicator still being used in log files
  • Issue 472: Don't report operator suggestions when autooptimize is on
  • Issue 473: BEAGLE default options should be CPU/Double
  • Issue 474: Partition table shows 0 taxa for trait partitions
  • Issue 478: TipDates table cell editor large the text font size when changing the value
  • Issue 479: Multi-block charset parsing and handling in BEAUTi
  • Issue 484: beagle_scaling command line flag turns on BEAGLE in the absence of any other flags
  • Issue 486: BEAST cannot find NucleotideLikelihoodCore.dll in Windows
  • Issue 487: BEAUti: Wrong error message with poorly constructed priors
  • Issue 488: BEAUti: Poor parsing of Poisson rate and offset in Priors
  • Issue 489: Default Laplace prior mean is 0.01
  • Issue 491: BEAUti parameter should keep uniform upper and lower
  • Issue 492: Should BEAUti use 'NNN' rather than 'N' for empty alignment, to allow for codon-partitioned models
  • Issue 494: BEAUti *BEAST does not need link tree prior option
  • Issue 495: Tree annotator needs to validate the duplicate taxon name

New in BEAST 1.6.1 (Nov 10, 2010)

  • Issue 398: BEAUti text message overlaps with button
  • Issue 399: Binary for TreeStat packaged with BEAST v1.6 has wrong version
  • number and icon
  • Issue 403: Starting tree generated with constraints by BEAUti is not correct
  • XML for BEAST
  • Issue 404: Make "Median heights" as the default of nodeHeightsCombo
  • Issue 405: RandomWalkOperator with reflecting boundary can grind to a halt
  • Issue 407: *BEAST needs to log species tree in { }, otherwise TreeAnnotator
  • keeps coming up with null exception on species tree
  • Issue 408: TreeAnnotator crashes with Null Pointer Exception on malformed
  • metacomment
  • Issue 410: "Improper priors" on posterior statistics
  • Issue 411: Incorrect validation and error message for random local clock in BEAUti
  • Issue 412: BEAUti generates randomWalkOperator instead of randomWalkIntegerOperator for branchRates.categories
  • Issue 413: BEAUti: duplicate class PartitionModelOptions causes model link conflict
  • Issue 414: BEAUti: incorrect xml for multi-alignment when given complex
  • combination of clock model and tree model
  • Issue 416: Laplace prior parser should use scale same as BEAUti
  • Issue 417: BEAUti growthRate related XML causes -INF likelihood
  • Issue 418: Set maximun fraction digits for numbers displayed in BEAUti prior panel
  • Issue 419: BEAUti RealNumberField should not throw Exception all the time
  • Issue 422: BEAUti: add validation to check whether modified prior initial value
  • is between the boundary

New in BEAST 1.6.0 (Nov 10, 2010)

  • New Features:
  • Random local clock model, see:
  • Drummond AJ and Suchard MA (2010) Bayesian random local clocks or one
  • rate to rule them all. BMC Biology.
  • Discrete trait models, see:
  • Lemey P, Rambaut A, Drummond AJ & Suchard MA (2009) Bayesian
  • Phylogeography Finds Its Roots.PLoS Comput Biol 5, e1000520.
  • http://beast.bio.ed.ac.uk/Tutorials#Phylogeography_tutorials
  • Continuous trait models, see:
  • Lemey P, Rambaut A, Welch JJ & Suchard MA Phylogeography takes a
  • relaxed random walk in continuous space and time. (2010)
  • Mol Biol Evol 27, 1877-1886.
  • These models are not currently specifiable from BEAUti, but see here:
  • http://beast.bio.ed.ac.uk/Tutorials#Phylogeography_tutorials
  • Improved user interface for Discrete Trait models in BEAUti.
  • Added an 'Include Stem?' option in the Taxon Set table in BEAUti.
  • This allows the calibration to be specified for the stem of a clade.
  • Added the application TreeStat to the BEAST package.
  • Can 'drag and drop' files to the data table in BEAUti to import them.
  • New 'tool tip' help messages for most user-interface elements in BEAUti
  • The name of the XML file is now shown in the title bar of the BEAST window.
  • By default, BEAST will no longer overwrite existing log/trees files. This behaviour can be overridden by using the '-overwrite' command line option or the check box in the options dialog box.
  • There is a BEAST new command line option '-prefix XXX' which will add the specified text to start of the file names of all log files and trees files for that run. This is useful for batch running of BEAST.
  • More warnings are given now about potentially problematic prior choices, in particular the use of improper priors. These are shown in yellow. For some models, the user now has to make an explicit prior choice.
  • Bug Fixes:
  • This version addresses the following issues:
  • Issue 40: TreeAnnotator produced misleading medians and HPDs when calculated from only 1 tree.
  • Issue 170: coalescentLikelihood would sometimes result in a zero initial likelihodo when using an UPGMA starting tree
  • Issue 235: BEAUti: Unlinked DiscretizedBranchRates for multiple loci have the wrong number of dimensions
  • Issue 291: BEAUti: fixed a problem generating a user specified starting tree
  • in XML.
  • Issue 298: BEAUti: checks that a user specified tree is rooted and fully bifurcating.
  • Issue 300: BEAUti: Simplified the XML for discrete models by using a single
  • 'generalSubstitutionModel' parser for all variants.
  • Issue 302: BEAUti: Now possible to importing multiple files at once when they
  • have different taxon sets
  • Issue 307: BEAUti: missing .txt in tree log using EBSP
  • Issue 311: BEAUti: Prior choices for codon partition parameters are now properly generated.
  • Issue 328: BEAUti: No longer generates very long default value and bound arrays for parameters.
  • Issue 332: BEAUti: Add traits now allows any trait name to be given.
  • Issue 333: BEAUti: Unlink buttons are enabled even when only one partition is loaded
  • Issue 337: BEAUti: Creating a 'CONTINUOUS' or 'INTEGER' trait gives Discrete model of substitution in SiteModelPanel
  • Issue 345: BEAUti: traits can be edited in the Traits table.
  • Issue 346: BEAUti: Show user a guide for an example of *BEAST or trait mapping file format.
  • Issue 347: BEAUti: Change for BEAUti default prior of ucld.stdv and kappa
  • Issue 348: BEAST: For GUI versions, then , should allow BEAST to continue running.
  • Issue 349: BEAUti: Window is too large for low resolution projector or screen.
  • Issue 352: BEAUti: NullPointerException if leave any trait value empty after activate BSSVS
  • Issue 353: BEAUti: *BEAST is now explicitly activated by a check box above the data partition table.
  • Issue 356: BEAUti: Added instructions to show user how to load specified starting tree from BEAUti
  • Issue 357: BEAST: Linux/UNIX version was unable to locate the native libraries.
  • Issue 361: BEAUti: RegEx for guess dates and guess traits now works better.
  • Issue 369: Beauti: Tip Dates panel: Tip date sampling "apply to" resets to
  • "All taxa" after navigating to different tab
  • Issue 374: BEAUti: only one taxon set for 3 unlinked partitions
  • Issue 380: BEAUti: Discrete trait model should have its tree linked to that for a tree for a sequence partition
  • Issue 381: BEAUti: Discrete trait model can select an inappropriate substitution model in the data partition table
  • Issue 383: BEAUti: "species" trait should not appear in Data Panel
  • Issue 384: BEAST: Unhandled attribute (typo?) name in sumStatistic:rateChanges
  • Issue 387: BEAUti: Generates wrong xml when a uniform prior is selected for species.popMean
  • Issue 391: BEAUti: add includeStem for taxon set

New in BEAST 1.5.4 (Nov 10, 2010)

  • Issue 52: Commas put into years displayed in BEAUti
  • Issue 59: examples/testCoalescent.xml
  • Issue 74: mcmc.operators
  • Issue 161: BEAUTi: review all initial rates and root heights calculations
  • Issue 162: Fix unstable JUnit test
  • Issue 198: Improper JUnit test code causes incorrect failure in Hudson
  • Issue 241: BEAUTi: operator subtreeSlide size should not be INF
  • Issue 270: BEASTParserDoc is unable to generate Wiki format
  • Issue 267: BEAUTi: The user should *always* be allowed to fix the rates if they want
  • Issue 268: BEAUti: prior distribution error message "find incorrect number format"
  • Issue 277: Typo in BEAUTi - Unable to overwrite exsting file
  • Issue 282: BEAUti: AlignmentGenerator cannot print sequence with long sites properly
  • Issue 285: BEAST: ComplexSubstitutionModelParser can only refer to SVS not ComplexSubstitutionModel
  • Issue 286: BEAUti: remove exponential in VariableDemographicModel from BEAUti
  • Issue 287: BEAUti: EBSP VariableDemographicModel popSize value = populationMean value and indicators value = 0
  • Issue 288: BEAUti: avoid comma generated in the numbers in the log

New in BEAST 1.5.3 (Nov 10, 2010)

  • New Features:
  • GUI versions of BEAST show a dialog box to set various options that are otherwise only available by command-line.
  • Bug Fixes:
  • This version addresses the following issues:
  • 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 1.5.2 (Nov 10, 2010)

  • New Features:
  • GUI versions of BEAST show a dialog box to set various options that are otherwise only available by command-line.
  • Bug Fixes:
  • Many bugs fixed that were introduced in 1.5.1 including:
  • 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
  • Issue 176: BEAUti: LogNormal mean should be > 0 when mean in real space
  • Issue 179: species.popSize is a horrible choice of name
  • Issue 180: BEAUTi: allMus is not dealing with multi-partition + codon, and
  • allClockRate
  • Issue 183: BEAUTi: clock model should use different mu with codon model
  • Issue 184: BEAUTi: make "mu" only appeared using codon model
  • Issue 185: Guess Trait dialog doesn't offer user defined traits
  • Issue 188: Suggestion to remove 'pre-burnin'
  • Issue 190: Mac app ant build needs several corrections
  • Issue 192: BEAUti: GUI exception when attempting to add a new trait
  • Issue 195: BEAUTi ignores and resets change of prior
  • Issue 196: Beast failure with file generated by BEAUTi (ucld)
  • Issue 197: meanRate, coefficientOfVariation and covariance should have gene name in name="" attribute
  • Issue 200: BEAUTi: *BEAST using Import Trait cannot add species in Trait table

New in BEAST 1.5.1 (Nov 10, 2010)

  • New Features:
  • BEAST: a version of BEAST that can estimate species trees from multi-locus multi-individual data sets using the multispecies coalescent (Heled & Drummond, 2009, submitted)
  • BEAUti overhaul: BEAUti has been completely re-written to allow flexible handling of multi-partition analyses, including partitioning by substitution models, clock models and trees. BEAUti also supports the new *BEAST method.
  • Relaxed clock refinements: The uncorrelated relaxed clock models have been refined by the addition of two new operators to address (valid) criticisms levelled in "Bayesian estimation of species divergence times from multiple loci using multiple calibrations", Rannala and Yang (2007). The change allows more than one branch to have the same relaxed clock rate category. In practice this will only have any appreciable impact on trees that have a small number of branches (< 15 taxa).
  • Added phylogeography models of Lemey et al (2009), PLoS Comput Biol.
  • Added post mortem damage models of Rambaut et al (2009) Mol Biol Evol.
  • Bug Fixes:
  • Issue 38: If partitions are unlinked then the base frequencies should be calculated from each partition separately;
  • Issue 80: ant build generates a broken beast;
  • Issue 81: ant build release fails after recent changes to beauti;
  • Issue 82: dr.app.util.Utils is broken (use of java 1.6 features?);
  • Issue 97: Remove "Link All/Unlink All" buttons from Data Tab;
  • Issue 98: Request to be able to view data partition alignments;
  • Issue 99: Suggestion: Clock Models tab;
  • Issue 100: Request to revise UI of "Choose Fix Rate Option";
  • Issue 103: Comments and suggestions for "MCMC Tab";
  • Issue 106: Single locus but multiple codon partitions: Doesn't allow 'Fixed mean rate';
  • Issue 109: BEAUti: Generating XML - no file overwriting warning?;
  • Issue 110: BEAUTi: excludedTaxonSetsComboBox and includedTaxonSetsComboBox in Taxon Sets panel not updating
  • Issue 114: Beauti Priors panel for starbeast;
  • Issue 115: Beauti starbeast: missing updown operator for first gene;
  • Issue 116: Make TN93 available in BEAUTi;
  • Issue 118: Beauti defaults - clock.rate in starbeast;
  • Issue 119: Beauti fails;
  • Issue 120: Beauti silliness - warn about not saving when nothing was done;
  • Issue 121: Beauti generates spurios multiple upDown operators;
  • Issue 124: Create method to check calibration situation;
  • Issue 125: Tree prior panel affecting isShareSameTreePrior check box wrongly.