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bump version number + list changes #1198 
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‎release/common/README.txt‎

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BEAST v2.7.7 2024
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Beast 2 development team 2011-2024
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BEAST v2.7.8 2025
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Beast 2 development team 2011-2025
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Last updated: June 2024
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Last updated: June 2025
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Contents:
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1) INTRODUCTION

‎release/common/VERSION HISTORY.txt‎

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BEAST v2.7.7 2024
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Beast 2 development team 2011-2024
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BEAST v2.7.8 2025
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Beast 2 development team 2011-2025
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Version History
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Last updated: June 2024
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Last updated: June 2025
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All issues can be viewed at https://github.com/CompEvol/beast2/issues
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================================================================================
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Version 2.7.8 June 2025
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o more robust state reconstruction in MCMC. #1201
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o improve tracability of XML errors (when spec has not been specified) #28
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o Methods for CLI repo management via packagemanager.
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o fix DeltaExchangeOperator, BactrianDeltaExchangeOperator, for weighted Dirichlet #1199
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o For initialisation & weighing for Dirichlet #1190
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o Substitution model RealParamter input to Function input conversions #1196
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o allow use of Coalescent without specifying TreeIntervals. #1192
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o split off Citable from BEASTInterface so it can be used independently. Facilitates BeastFX#94
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o enable uncertain alignments to be filtered by FilteredAlignment. #1188
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o fix error reporting of BactrianDeltaExchangeOperator. #1187
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o fix for direct simulating from integer distribution #1186
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o restore frequencies warning statement #1185
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o make BactrianOperatorSchedule ignore Uniform operators if parameter is not a RealParameter #1183
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o add public method to GeneralSubstitutionModel #1181
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o robustify tree likelihoods for possibility data is not Alignment #1174
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o make TreeWithMetaDataLogger produce correct nr of commas. #1177
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o add benchmark interface to BeagelTreeLikelihood #1172
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o towards renaming scaleFactor to windowSize in BactrianRandomWalkOperator #1169
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o fix indexing error in beagle tree likellihood #1168
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o set ids of trees parsed from NEXUS file. BeastFX#87
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o facilitate beast "-validate" option BeastFX#86
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o Adds CL packagemanager option to add repositories. Closes #1163
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o update parameter dimension on -resume #1159
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o improve error message for XML where the spec attribute is missing #28
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o deal with spaces in quoted attribute values #30
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o make alignments non-clonable for BEAUti link/unlink support #1150
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o redirect output to stderr in order to prevent it getting redirected to files (e.g. citations in TreeAnnotator) BeastFX#98
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o make Application validate Inputs after setting Input values. BeastFX#97
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o add Description to TreeAnnotator, which shows when running treeannotator -help #28
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o add support for citing methods in TreeAnnotator BeastFX#94
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o Fixing #92 GUI dropdown not closing on first selection
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o replace colons by dashes in IDs named by file name. #1184
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o add more sensible OutOfMemmoryError messages to TreeAnotator #28
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o fix renaming id's when cloning site model. BeastFX#91
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o set IDs of parsed trees in tree set BeastFX#87
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o improve error handling for upgrading packages missing from repositories. #1166
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o enhance beast "-validate" option. BeastFX#86
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o fix threading when running LogAnalyser with threads. BeastFX#81
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o fix -version_file bug #1158
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o add -version_file option to AppLauncher #1158
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o make Newick parser work for MemoryFriendlyTreeSet. BeastFX#85
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o add -includeEvery option to LogCombiner BeastFX#84
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o fix issue with link/unlink parittions in BEAUti. BeastFX#83
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Version 2.7.7 June 2024
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o Add CCD to the list of recommended packages for TreeAnnotator CompEvol/beast2#1138
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TreeAnnotator GUI to pick up correct topology setting method CompEvol/beast2#1143

‎src/beast/base/core/BEASTVersion2.java‎

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/**
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* Version string: assumed to be in format x.x.x
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*/
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private static final String VERSION = "2.7.7";
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private static final String VERSION = "2.7.8";
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private static final String DATE_STRING = "2002-2024";
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private static final String DATE_STRING = "2002-2025";
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private static final boolean IS_PRERELEASE = true;
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//

‎src/beast/pkgmgmt/BEASTVersion.java‎

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/**
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* Version string: assumed to be in format x.x.x
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*/
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private static final String VERSION = "2.7.7";
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private static final String VERSION = "2.7.8";
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private static final String DATE_STRING = "2002-2024";
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private static final String DATE_STRING = "2002-2025";
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private static final boolean IS_PRERELEASE = true;
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‎version.xml‎

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<package name="BEAST.base" version="2.7.7">
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<package name="BEAST.base" version="2.7.8">
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<!-- note version="2.7.x" must be double quotes for Mac release script release/Mac/createdmg.sh -->
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<!-- data types -->

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