Issues

• Using -beagle_auto on an Apple Silicon mac fails to create a BEAGLE Kernel.

  BEASTbug
  Bug

  beast-dev/beast-mcmc#1270 · Filter by author rambaut opened on Sep 14, 2026
  2

• MacOS GUI fails to write checkpoint files specified in XML

  beast-dev/beast-mcmc#1268 · Filter by author hongsamL opened on Sep 2, 2026

• In BEAUti v10.5.0 Taxon Set options not passing to xml file

  beast-dev/beast-mcmc#1266 · Filter by author KWollenbergPhylo opened on Aug 12, 2026

• Importing taxa files to beauti locks 'Trees' tab preventing editing

  beast-dev/beast-mcmc#1263 · Filter by author matbeale opened on Jul 6, 2026

• Poisson likelihood computed outside log-space causes numerical underflow (Thorney strict clock)

  beast-dev/beast-mcmc#1249 · Filter by author Jujuke opened on Jan 20, 2026
  1

• Setting burnin in LogCombiner v10.5.0

  beast-dev/beast-mcmc#1247 · Filter by author MarliesJFrancine opened on Dec 15, 2025
  3

• Starting tree constraints without monophyly constraints on taxa partitions

  beautienhancement
  beast-dev/beast-mcmc#1246 · Filter by author plemey opened on Nov 12, 2025 · v10.6.0

• handling multiple partitions with codonPartitionedRobustCounting & dNdSLogger

  beauti
  Feature

  beast-dev/beast-mcmc#1241 · Filter by author plemey opened on Sep 5, 2025

• Branch 'beauti_subtree_prior' - can't create local clock and subtree prior

  beautibug
  Bug

  beast-dev/beast-mcmc#1231 · Filter by author rambaut opened on May 15, 2025 · v10.6.0
  

• Fix checkpointing for relaxed clock models

  bug
  Bug

  beast-dev/beast-mcmc#1225 · Filter by author GuyBaele opened on Apr 21, 2025
  

• Issue Thorney-beast with relax clock model

  beast-dev/beast-mcmc#1217 · Filter by author AlbertoA3 opened on Feb 4, 2025

• HMC Clock Model doesn't produce any mention or citation

  enhancement
  beast-dev/beast-mcmc#1190 · Filter by author rambaut opened on Jul 12, 2024 · v10.6.0

• Put more information in the operator log

  enhancement
  beast-dev/beast-mcmc#1187 · Filter by author rambaut opened on Jun 16, 2024 · beast X
  1

• Idea: Get BEAUti to load an operator log and use it to weight the operators

  enhancement
  beast-dev/beast-mcmc#1186 · Filter by author rambaut opened on Jun 16, 2024 · beast X

• Update/fix example files

  help wanted
  beast-dev/beast-mcmc#1177 · Filter by author rambaut opened on Apr 27, 2024 · beast X

• Covariates for skygrid in BEAuti

  beautienhancement
  beast-dev/beast-mcmc#1169 · Filter by author plemey opened on Mar 6, 2024 · beast X
  

• Using the AutocorrelatedClock

  bug
  beast-dev/beast-mcmc#1101 · Filter by author sebastianduchene opened on Dec 7, 2020 · beast X

• Parsing error for BEAUTi-generated xml file for directional random walk model

  beautibug
  beast-dev/beast-mcmc#1083 · Filter by author mlewinsohn opened on May 5, 2020 · v10.6.0
  2

• Can not fully use GPU?

  bug
  beast-dev/beast-mcmc#1079 · Filter by author LauraVP1994 opened on Jan 23, 2020 · beast X
  8

• issue with data simulation under codon Markov-modulated model

  enhancement
  beast-dev/beast-mcmc#1078 · Filter by author GuyBaele opened on Jan 19, 2020 · beast X
  

• Checkpointing does not seem to work with Markov-modulated models

  bug
  beast-dev/beast-mcmc#1072 · Filter by author GuyBaele opened on Sep 17, 2019 · beast X
  1

  

• Importing partition information in BEAUti 1.10.x

  beautibug
  beast-dev/beast-mcmc#1066 · Filter by author GuyBaele opened on Jul 23, 2019 · beast X
  1

  

• XML contains HPM that are not shown in the prior window

  beautibug
  beast-dev/beast-mcmc#1062 · Filter by author Serebix opened on Jun 7, 2019 · beast X

• Migrate Ancestral States and Markov Jumps to TreeDataLikelihood

  BEASTenhancementhelp wanted
  beast-dev/beast-mcmc#1059 · Filter by author rambaut opened on May 17, 2019 · beast X
  1

  

• Implement Muse & Gaut codon model selection in BEAUti.

  beautienhancement
  beast-dev/beast-mcmc#1057 · Filter by author rambaut opened on May 2, 2019 · beast X