Issues

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

  BEASTbug
  Bug

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

• Fix checkpointing for relaxed clock models

  bug
  Bug

  beast-dev/beast-mcmc#1225 · Filter by author GuyBaele opened on Apr 21, 2025 · v10.6.0
  1

  

• 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

• 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

  BEASTbeautienhancement
  Feature

  beast-dev/beast-mcmc#1101 · Filter by author sebastianduchene opened on Dec 7, 2020 · beast X
  1

• 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
  

• 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

• Make thread control behaviour more intuitive

  BEASTenhancement
  beast-dev/beast-mcmc#1039 · Filter by author rambaut opened on Nov 13, 2018 · beast X
  1

• Code signing for Windows exe

  enhancement
  beast-dev/beast-mcmc#1034 · Filter by author rambaut opened on Sep 30, 2018 · beast X

• Tooltips for LogCombiner and TreeAnnotator

  beast-dev/beast-mcmc#1028 · Filter by author rambaut opened on Sep 17, 2018 · beast X

• Need way of specifying tip local clocks in BEAUti

  beautienhancement
  beast-dev/beast-mcmc#1012 · Filter by author rambaut opened on Aug 13, 2018 · beast X
  

• Debug dump doesn't work with skygrid+covariates+BSSVS

  beast-dev/beast-mcmc#992 · Filter by author GuyBaele opened on May 29, 2018 · beast X
  

• 'Link tree prior' option is inconsistent

  beautienhancement
  beast-dev/beast-mcmc#954 · Filter by author rambaut opened on Sep 2, 2017 · beast X

• Need scaled logit for generalized stepping-stone sampling?

  enhancement
  beast-dev/beast-mcmc#953 · Filter by author GuyBaele opened on Aug 31, 2017 · beast X
  1

  

• Check for 0s or (0/1s) in BEAUti GLM import

  beautienhancement
  beast-dev/beast-mcmc#952 · Filter by author msuchard opened on Aug 31, 2017 · beast X
  3

  

• Set appropriate bounds on rates in ArbitraryBranchRates

  beast-dev/beast-mcmc#948 · Filter by author msuchard opened on Aug 30, 2017 · beast X
  

• HPM operators in BEAUti

  beautienhancement
  beast-dev/beast-mcmc#930 · Filter by author GuyBaele opened on Aug 13, 2017 · beast X
  1

  

• Add half a year to sampling date when performing tip date sampling

  enhancement
  beast-dev/beast-mcmc#919 · Filter by author GuyBaele opened on Aug 2, 2017 · beast X
  1

  

• Add covariates for skygrid in BEAUti

  beautienhancement
  beast-dev/beast-mcmc#918 · Filter by author rambaut opened on Aug 2, 2017 · beast X
  3

• Add fixed effects on rates or hierarchical parameters.

  beautienhancement
  beast-dev/beast-mcmc#917 · Filter by author rambaut opened on Aug 2, 2017 · beast X

• Test priors on alpha parameter of discrete gamma heterogeneity using simulation

  BEASTenhancement
  beast-dev/beast-mcmc#908 · Filter by author rambaut opened on Jul 20, 2017 · beast X