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Recent Releases of https://github.com/compevol/beast2

https://github.com/compevol/beast2 - Version v2.7.8 release

This is a package release only -- to install, install v2.7.7 and update the BEAST.base and BEAST.app packages. ```

BEAST

o fix DeltaExchangeOperator, BactrianDeltaExchangeOperator, for weighted Dirichlet #1199
o For initialisation & weighing for Dirichlet #1190

o facilitate beast "-validate" option BeastFX#86
o fix for direct simulating from integer distribution #1186
o enhance beast "-validate" option. BeastFX#86
o make TreeWithMetaDataLogger produce correct nr of commas. #1177
o make BactrianOperatorSchedule ignore Uniform operators if parameter is not a RealParameter #1183
o update parameter dimension on -resume #1159
o deal with spaces in quoted attribute values BeastFX#30
o make Newick parser work for MemoryFriendlyTreeSet. BeastFX#85

BEAUti

o fix issue with link/unlink parittions in BEAUti. BeastFX#83
o fix renaming id's when cloning site model. BeastFX#91
o replace colons by dashes in IDs named by file name. #1184
o make alignments non-clonable for BEAUti link/unlink support #1150

TreeAnnotator

o Fixing BeastFX#92 GUI dropdown not closing on first selection

Other apps

o add -includeEvery option to LogCombiner BeastFX#84
o add -version_file option to AppLauncher #1158
o fix threading when running LogAnalyser with threads. BeastFX#81
o make Application validate Inputs after setting Input values. BeastFX#97
o set IDs of parsed trees in tree set BeastFX#87

For developers

o more robust state reconstruction in MCMC. #1201
o allow use of Coalescent without specifying TreeIntervals. #1192
o add public method to GeneralSubstitutionModel #1181

o add Description to TreeAnnotator, which shows when running treeannotator -help BeastFX#28
o add support for citing methods in TreeAnnotator BeastFX#94
o split off Citable from BEASTInterface so it can be used independently. Facilitates BeastFX#94
o Substitution model RealParamter input to Function input conversions #1196
o robustify tree likelihoods for possibility data is not Alignment #1174
o add benchmark interface to BeagelTreeLikelihood #1172
o towards renaming scaleFactor to windowSize in BactrianRandomWalkOperator #1169
o fix indexing error in beagle tree likellihood #1168
o redirect output to stderr in order to prevent it getting redirected to files (e.g. citations in TreeAnnotator) BeastFX#98

Improved error messages

o improve tracability of XML errors (when spec has not been specified) #28
o fix error reporting of BactrianDeltaExchangeOperator. #1187
o improve error handling for upgrading packages missing from repositories. #1166
o add more sensible OutOfMemmoryError messages to TreeAnotator BeastFX#28
o improve error message for XML where the spec attribute is missing BeastFX#28
o restore frequencies warning statement #1185

```

- Java
Published by rbouckaert 12 months ago

https://github.com/compevol/beast2 - v2.7.7 pre release

FOR TESTING ONLY 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

- Java
Published by rbouckaert almost 2 years ago

https://github.com/compevol/beast2 - Release v2.7.6pre

DO NOT USE!

For testing purposes only

- Java
Published by rbouckaert over 2 years ago

https://github.com/compevol/beast2 - 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

```

- Java
Published by rbouckaert almost 3 years ago

https://github.com/compevol/beast2 - 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

- Java
Published by rbouckaert about 3 years ago

https://github.com/compevol/beast2 - 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

- Java
Published by rbouckaert over 3 years ago

https://github.com/compevol/beast2 - BEAST.base 2.7.2

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

- Java
Published by jordandouglas over 3 years ago

https://github.com/compevol/beast2 - 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

- Java
Published by rbouckaert over 3 years ago

https://github.com/compevol/beast2 - 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

- Java
Published by rbouckaert almost 4 years ago

https://github.com/compevol/beast2 - 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

- Java
Published by rbouckaert about 4 years ago

https://github.com/compevol/beast2 - 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

- Java
Published by rbouckaert almost 5 years ago

https://github.com/compevol/beast2 - BEAST v2.6.5 release

Patch release that fixes output bug introduced in the GUI version of LogCombiner in v2.6.4.

To install, first install v2.6.4, then upgrade using the package manager, or by starting BEAUti, which automatically checks for updates.

- Java
Published by rbouckaert almost 5 years ago

https://github.com/compevol/beast2 - BEAST v2.6.4 release 

Applauncher picks up BEAGLE
Less clutter on screen output
Bayesian skyline plot has a proper prior alternative for the first element of the popSizes parameter
Fix DensiTree launcher for Windows & Mac
LogCombiner can now write to stdout
FilteredAlignment can deal with missing and ambiguous values
Node now recognises age trait
Allow packages to be released in github release area again
Add differentRandomIndex to UpDownOperator
Checksum support for developers chasing incorrectly calculated likelihoods

- Java
Published by rbouckaert over 5 years ago

https://github.com/compevol/beast2 - BEAST v2.6.3 release 

    Robustify resume
    RandomTree deals with calibrations in date-forward mode
    BEAST new `-DF` and `-DFout` options
    Default values for user defined values
    LogAnalyser new `-tag` option
    Let `Input.setValue()` ignore empty lists (instead of throwing exception)
    User data type lengths are not required to be equal any more
    Robustify RPN calculator

- Java
Published by rbouckaert about 6 years ago

https://github.com/compevol/beast2 - BEAST v2.6.2 release 

    Allow operator schedule changes in BEAUti
    Fix quantile parameterisation of relaxed clocks
    Add batch file for Windows command line usage
    Improve error messages
    Provide better access in API for developers

- Java
Published by rbouckaert over 6 years ago

https://github.com/compevol/beast2 - BEAST v2.6.1 release

  • Fixes bug in BEAUti so that template of "last" package is recognised
  • Makes loganalyser deal with spacees in trace log names
  • Adds column to LogAnalyser -oneline output
  • Has random local clock fix for unscaled rates

More details are available here: http://www.beast2.org/2019/08/08/what-is-new-in-v2.6.1.html

- Java
Published by rbouckaert almost 7 years ago

https://github.com/compevol/beast2 - BEAST v2.6.0

Main changes

    Robustify application launching and package upgrading (especially for Windows)
    Faster BEAUti processing of large number of partitions

Other changes

    Make sequenceSimulator less sensitive to taxa ordering
    Improved error messages
    XML being produced is more standardised
    Make help menu extendible to add for example automatic methods section generator        
    Saves last accessed directory between sessions
    Default bounds on BSP pop sizes and random local clock rates updated
    Let GuessPatternDialog handle empty fields.
    Adding MRCAPriors more robust when multiple alignments share a tree
    More complete Nexus parser

For developers

    More flexible options for constructing BEAST objects 
    More access methods to core classes
    Added BEASTInterface::notClonable

There are more details for users and developers on the beast2.org website.

- Java
Published by rbouckaert about 7 years ago

https://github.com/compevol/beast2 - BEAST 2.5.2

  • More robust release for Windows that includes JRE
  • Fix AppLauncher for OS X
  • Robustify start scripts for OS X, Linux
  • Implement rate parameterisation for uncorrelated relaxed clock model
  • Improved error messages
  • Relaxed API giving more access to package developers
  • Node.getMetaData() now returns null on key not found
  • Pass -Xss arguments through launchers to set stack size
  • DOIs point to preferred resolver
  • Fix multi-threading issue with parameteric distributions
  • Remove posterior ESS from screen log

- Java
Published by rbouckaert over 7 years ago

https://github.com/compevol/beast2 - BEAST 2.5.1

Add -X flag to all applications, so more memory can be allocated Fix some OS X with Java 9+ anomalies More robust OS X CUDA check More robust launch scripts Better error reporting More robust package manager TreeAnnotator handles taxa that are numbers now Allow multiple -D arguments to BEAST, allows commas in user defined variables

- Java
Published by rbouckaert almost 8 years ago

https://github.com/compevol/beast2 - BEAST 2.5.0

Note that if you use this, there may be packages that are still not available. If you need to use an unavailable package, you can use BEAST v2.4.8 instead.

- Java
Published by rbouckaert about 8 years ago

https://github.com/compevol/beast2 - BEAST 2.4.8

Ensure BeagleTreeLikelihood gives correct likelihood with RNA data.

- Java
Published by rbouckaert almost 9 years ago

https://github.com/compevol/beast2 - BEAST 2.4.7

BEAUti

Relabel buttons: "Guess" is now "Auto configure" in tip dates panel. "+" button on priors panel is now "+ Add Prior".
More sensible default date value for taxa without date specified in tip dates panel.
Make sure the appropriate tree is used in MRCAprior.
Make sure tips with 'fixed' distributions imported from Nexus do not get estimated.
Robustify NEXUS parser.
Taxa could be duplicated in taxon list in NexusParser.
Prevent accidentally cloning of up-down-all operator in StarBeast.

BEAST

Default locale set to english so full stops are used in NEXUS output.
Warn if Yule (or BD) conditions on root, but no root MRCAPrior is set.
Robustify resume 
Suppress "Overwrite (Y/N)?" message when BEAST runs in console.
Stop chain when encountering a +infinity posterior.
Check that taxon set is specified when using RandomTree.
Normalise stateNodes so XML characters ('"&<>) get escaped properly when writing state files.

Appstore

Improved formatting of app list.

TreeAnnotator 

Now adds common ancestor height estimates as attributes.

API updates:

Changed access levels of a few methods in nexus parser.
Add Tree scale and ScaleOperator test.
Add new Tree constructor from root node.
Add support for input/output of non-binary trees.
Add Input.set() method.
BeautiAlignmentProvider getAlignments method added to facilitate scripting.
TreeParser correctly parses tree edge length metadata, and improved error reporting.

- Java
Published by rbouckaert almost 9 years ago

https://github.com/compevol/beast2 - BEAST 2.4.6 

BEAUti
    Starting trees can now be edited (default random, choice of cluster and newick trees)
    Allow alignments to be replaced, so old analyses can be used for new data
    Fix fasta file import bug that marked sequences as amino acid while it should be nucleotide
    Keep trees linked when splitting alignment on codon positions
    Automatically set estimate flag on shape when choosing rate categories
    Fix display of integer alignments

BEAST
    Better documentation
    More robust XMLParser
    Prevent double counting of offset in ParametricDistribution.sample

DensiTree version updated to v2.2.6

- Java
Published by rbouckaert about 9 years ago

https://github.com/compevol/beast2 - BEAST 2.4.5 

   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

- Java
Published by rbouckaert over 9 years ago

https://github.com/compevol/beast2 - BEAST 2.4.4

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.

- Java
Published by rbouckaert over 9 years ago

https://github.com/compevol/beast2 - BEAST 2.4.3

``` 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 ```

- Java
Published by rbouckaert almost 10 years ago

https://github.com/compevol/beast2 - BEAST 2.4.2

``` 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 ```

- Java
Published by rbouckaert almost 10 years ago

https://github.com/compevol/beast2 - BEAST 2.4.1

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

- Java
Published by rbouckaert about 10 years ago

https://github.com/compevol/beast2 - BEAST 2.4.0

``` BEAST improved performance up to 2x faster when using proportion invariant sites improved threading support
"instances" flag replaces beagle_instances faster MRCAPrior handling StartBeastStartState works with calibrations with other than CalibratedYule

BEAUti show mean of parametric distributions in priors panel better taxon management preventing adding numbers to taxon names improved layout tip dates panel improved package list errors *BEAST clock cloning fix Allow setting branch length as substitution option on tree logger Improved JSON support

Package manager Allow BEAST to be upgraded as a package Improved GUI

For developers: http://beast2.org/2016/02/04/what-will-change-in-v2-4-0-for-developers/ ```

- Java
Published by rbouckaert over 10 years ago

https://github.com/compevol/beast2 - BEAST 2.3.3 prerelease

BEAST 2.3.3 prerelease

- Java
Published by rbouckaert over 10 years ago

https://github.com/compevol/beast2 - BEAST 2.3.2 release

``` BEAUti path corrected so Standard and StarBeast templates are visible under templates menu import of traits from file when partitions are split fixed cloning of scripts with partition information fixed set up weights of FixedMeanRate operator when ascertainment correction is applied allows ParameterInputEditor to edit Parameter inputs

BEAST
        add "-validate" command line option for parsing XML files without running them
        more efficient MRCAPrior
        more robust RandomTree

LogCombiner
        ensured logcombiner burn in editing finished properly

LogAnalyser now has one line per file mode, and CLI script added for ease of launch

More sensible error messages (in TreeParser, RPNCalculator, NodeReheight, and more).

```

- Java
Published by rbouckaert over 10 years ago

https://github.com/compevol/beast2 - BEAST 2.3.1 release

Note: requires Java 8.

``` BEAUti fixes robustify (un)linking improved Fasta import

BEAST
   support for uncertain alignments (see examples/testJukesCantorShortUncertain.xml) 
   improved error messages

TreeAnnotator allows lower memory consumption

AppStore, LogCombiners, LogAnalyser improved command line interface 

Antlr based tree parsing

DensiTree updated to v2.2.3

BinaryCovarion model option to run as reversible model 

Set log level by environment variable

```

- Java
Published by rbouckaert almost 11 years ago

https://github.com/compevol/beast2 - BEAST 2.3.0 release

BEAUti fixes cloning, linking, unlinking bugs fixed more robust templates calibrations can be deleted now improved access to package folders improved import menu

LogCombiner improved command line interface

Fix synchronisation issues affecting ThreadedTreeLikelihood

Auto load beast.jar, giving footprint for Mac

Bug fix in EigenDecomposition affecting asymmetric rate matrices

Reduced dependency on taxon order making multiple partition handling more robust

Can keep running v2.2 and its packages alongside v2.3

DensiTree updated to v2.2.2

- Java
Published by rbouckaert about 11 years ago

https://github.com/compevol/beast2 - BEAST 2.2.1 release

BEAUti some bug fixes involved in linking/cloning + some cosmetic changes

Better error reporting: - in BEAUti, estimate of relative substitution rate for single partition only caused BEAST to hang - check correct java version (8) is used - package manager warns when there is no internet connection

Improved NEXUS Standard datatype support

TreeAnnotator improved sampled ancestor support

CLI script now sensitive to JAVA_HOME environment variable

DensiTree updated to v2.2.1

- Java
Published by rbouckaert about 11 years ago

https://github.com/compevol/beast2 - BEAST v2.2.0 release

NOTE: you need Java 8 to run BEAST (freely available from http://java.com/)

Version 2.2.0 January 2015

``` Uses Java 8 to facilitate package development, thus preventing version clashes with packages

BEAUti default settings preventing common errors, template fixes, layout enhancements, error logging

Enhanced package manager

Better error reporting for finding common issues with XML files (such as *BEAST gene trees not covering all species)

Improved install for Mac

Over 300 commits for small bug fixes and performance enhancements (more readable XML, better NEXUS parsing, TreeAnnotator fix, etc.) ```

- Java
Published by rbouckaert over 11 years ago

https://github.com/compevol/beast2 - BEAST v2.2.0 pre-release

Pre-release, for the adventurous only...

- Java
Published by rbouckaert almost 12 years ago

https://github.com/compevol/beast2 - BEAST v2.1.3 release

Version 2.1.3 May 2014 Patch release

``` *BEAST template fixed

add AppStore for conveniently launching applications from packages

improved FASTA support

a few small fixes (BEAUti displays of log normal and other distributions, monophyletic constraint logging, allow import of alignments with same name in BEAUti,etc.) ```

The beastEBSP.jar and beastEBSP.src.jar contain a fix for the EBSP analyser, which can be run standalone.

- Java
Published by rbouckaert about 12 years ago

https://github.com/compevol/beast2 - BEAST v2.1.2 release

RELEASE 2.1.2 -- NOTE: the StarBeast template is broken-- do not use for *BEAST analysis

Patch release o BEAUti handles multiple partitions more conveniently o improved package management o fix bug in *BEAST template o many small fixes (FASTA support, stochastic distributions, *BEAST operator weighting, etc.)

- Java
Published by rbouckaert about 12 years ago

https://github.com/compevol/beast2 - BEAST v2.1.1 release

Patch release speeding up BEAUti to handle large Nexus files and handle multiple files.

- Java
Published by rbouckaert over 12 years ago

https://github.com/compevol/beast2 - BEAST v2.1.0 release

- Java
Published by tgvaughan over 12 years ago

https://github.com/compevol/beast2 - BEAST v2.0.2 release

- Java
Published by tgvaughan over 12 years ago