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