When BEAST migrated from version 2.6 to 2.7, the structure of its code base (and accordingly, its XML element specs) changed slightly. In particular, the AncestralSequenceLogger class that used to be in the beast/evolution/likelihood directory is no longer included in the core code base at all. It is now part of the BEAST-classic package.
When I wrote teiphy's BEAST XML output template, I was not aware of this, and I mistakenly had the template use AncestralStateLogger elements from the BEASTLabs package. The template should be corrected to use elements with spec="beastclassic.evolution.likelihood.AncestralSequenceLogger" instead of ones with spec="beastlabs.evolution.likelihood.AncestralStateLogger". More broadly, the ancestral sequence loggers should follow the template below:
When BEAST migrated from version 2.6 to 2.7, the structure of its code base (and accordingly, its XML element specs) changed slightly. In particular, the
AncestralSequenceLoggerclass that used to be in thebeast/evolution/likelihooddirectory is no longer included in the core code base at all. It is now part of theBEAST-classicpackage.When I wrote
teiphy's BEAST XML output template, I was not aware of this, and I mistakenly had the template useAncestralStateLoggerelements from theBEASTLabspackage. The template should be corrected to use elements withspec="beastclassic.evolution.likelihood.AncestralSequenceLogger"instead of ones withspec="beastlabs.evolution.likelihood.AncestralStateLogger". More broadly, the ancestral sequence loggers should follow the template below: