BEAST X v10.6.0-beta5

BEAST X v10.6.0 (in development)

New features

BEAUti

• Added option to write doubling time in days to the log file when using a coalescent model with an exponential growth parameter.
• Added an option to write the epidemiological reproduction number (R0) to the log file when using a coalescent model with an exponential growth parameter. This requires an estimate of the mean and standard deviation of the generation time distribution to be specified in BEAUti.

TreeAnnotator

• Can specify multiple HPD intervals e.g., using `--hpd 0.95,0.90,0.5'
• Can generate a KDE curve of the distribution of height values for visualisation in PearTree
• Clade MRCA heights can be calculated to avoid negative branch lengths (CA method of Heled and Bouckaert, (2013))

Bug fixes

BEAST

• Shows console window when running in Windows GUI version.

TreeAnnotator

• Fixed TreeAnnotator not summarising 2-dimensional locations correctly —
  continuous phylogeographic location traits (e.g. location1 / location2)
  were being renamed to location.rate1 / location.rate2 in the annotated
  tree output.
  (#1242)

• Fixed performance regression in TreeAnnotator "Collecting node information"
  stage — processing of large tree sets became increasingly slow and eventually
  stalled, a regression introduced after Beta5.
  (#1233)

• Fixed bug in TreeAnnotator for continuous phylogeography with fixed trees —
  coordinate annotations were being replaced by branch lengths and then discarded
  when the input tree topology was fixed rather than sampled.
  (#1255)

BEAUti

• Fixed BEAUti reverting clock-rate prior to CTMC reference prior — custom
  rate priors (e.g. a lognormal prior on the substitution rate) specified in
  BEAUti were being silently replaced by the CTMC reference prior when the XML
  was written.
  (#1238)

• Fixed an issue where if the name stem was too long, the names of the log files and tree files could be truncated in the XML.

Other changes

• Updated HIPSTR citation to the final published paper.
  (#1243)

Full Changelog: v10.5.0...v1.6.0-beta5

What's Changed

• Modern arguments by @rambaut in #1216

New Contributors

• @rambaut made their first contribution in #1216

Full Changelog: v10.5.0...v10.6.0-beta5