Issues

• How should equilibrium frequencies be handled in a GeneralSubstitutionModel with a potentially non-time-reversible rate matrix?

  CompEvol/beast2#1217 · Filter by author jjmccollum opened on Sep 27, 2026
  1

• For GeneralSubstitutionModel, use Padé approximant if matrix is non-diagonalizable or ill-conditioned

  CompEvol/beast2#1216 · Filter by author jjmccollum opened on Sep 25, 2026
  2

• Bundled Java runtime in BEAST 2.7.x releases has known vulnerabilities

  CompEvol/beast2#1215 · Filter by author berkleycam opened on Jun 16, 2026
  2

• EpochFlexOperator causes infinite loop/livelock when applied to 2-trees

  CompEvol/beast2#1214 · Filter by author dpascall opened on May 24, 2026

• AppLauncher should remain in headless mode when running from CLI with arguments

  CompEvol/beast2#1212 · Filter by author rbouckaert opened on Mar 24, 2026

• State.robustlyCalcPosterior calls store() as a side effect

  CompEvol/beast2#1211 · Filter by author alexeid opened on Mar 6, 2026

• java.lang.NullPointerException: Cannot invoke "Object.getClass()" because "<local3>" is null

  CompEvol/beast2#1208 · Filter by author genesandbones opened on Nov 9, 2025
  7

• Running BEAST from command line fails when arguments contain spaces

  CompEvol/beast2#1205 · Filter by author jugne opened on Sep 9, 2025

• Add tree annotator settings to output as comments

  CompEvol/beast2#1204 · Filter by author SimonGreenhill opened on Aug 15, 2025

• Exception in thread "main" java.lang.NullPointerException: Cannot invoke "java.net.URL.openConnection()" because "<local8>" is null

  CompEvol/beast2#1197 · Filter by author Gipsy-The-Sheller opened on May 31, 2025
  1

• Use Function in all inputs of SiteModel

  enhancement
  CompEvol/beast2#1196 · Filter by author walterxie opened on May 22, 2025
  5

• BEAUti Tip Date panel does not show Nexus configuration

  BEAUtidefect
  CompEvol/beast2#1194 · Filter by author walterxie opened on May 18, 2025
  2

• Restrict the location of clade MRCAs

  CompEvol/beast2#1193 · Filter by author sbenvari opened on May 15, 2025
  22

• generalise Dirichlet Distribution to deal with vectors that do not sum to 1

  CompEvol/beast2#1190 · Filter by author EvaLiyt opened on May 8, 2025
  3

• BactrianIntervalOperator incompatible with integer parameters

  CompEvol/beast2#1183 · Filter by author sgtRoberty opened on Mar 4, 2025
  1

• Beast2 fails with EigenDecompositionCube

  CompEvol/beast2#1182 · Filter by author aaron-wes opened on Feb 27, 2025
  7

• Issues with Treeannotator 2.7.7

  CompEvol/beast2#1178 · Filter by author lilychughes opened on Feb 4, 2025
  1

• Beast 2 home dir problem

  CompEvol/beast2#1175 · Filter by author hrzolix opened on Dec 19, 2024
  3

• Refactor Alignment

  CompEvol/beast2#1174 · Filter by author rbouckaert opened on Dec 12, 2024

• Associate data with internal nodes via IDs

  CompEvol/beast2#1173 · Filter by author rbouckaert opened on Nov 24, 2024
  2

• Enhance BEAGLE options

  CompEvol/beast2#1172 · Filter by author rbouckaert opened on Oct 30, 2024

• Loading of file.xml failed. Cannot read the array length because "this.patternIndex" is null.

  CompEvol/beast2#1171 · Filter by author mrmancuso opened on Oct 24, 2024
  1

• BactrianRandomWalkOperator should use "windowSize"

  CompEvol/beast2#1169 · Filter by author walterxie opened on Sep 29, 2024 · 2.8

• java.lang.NullPointerException: Cannot invoke "beast.base.evolution.tree.Node.isRoot()" because "<parameter1>" is null

  CompEvol/beast2#1162 · Filter by author liamxg opened on Aug 28, 2024

• Add case to Tree.adjustTreeNodeHeights method to accommodate zero-length branches

  CompEvol/beast2#1161 · Filter by author jjmccollum opened on Aug 12, 2024