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1. Commits on Aug 6, 2026

   • mv to compevol

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   • Merge pull request #12 from BEAST2-Dev/main

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   • correct release and CI

     walterxie

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2. Commits on Jul 5, 2026

   • Merge pull request #11 from kche309/main

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     rbouckaert

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   • Update tree likelihood classes to beast3 spec version and unit tests

     kche309

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   • Merge pull request #10 from kche309/main

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     rbouckaert

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3. Commits on Jul 2, 2026

   • patch bugfix for store restore methods in MATreeLikelihood and BeagleMATreeLikelihood from branch alexeid:fix-store-restore-for-mutable-tips-beast27

     kche309

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4. Commits on Apr 12, 2026

   • Merge pull request #7 from alexeid/beast3

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5. Commits on Apr 1, 2026

   • Fix tests: migrate JUnit 4 to 5, inline BEASTTestCase.PRECISION, remove dead code

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     alexeid

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6. Commits on Mar 31, 2026

   • Bring package up to beast3 gold standard

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     alexeid

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   • Update README for beast3: Maven coordinates, module name, cleanup

     alexeid

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   • Flatten to single-module Maven project, rename artifact and JPMS module

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     alexeid

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   • Migrate MATreeLikelihood to spec TreeLikelihood

     alexeid

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7. Commits on Mar 20, 2026

   • Add module-info.java: module beast.mutable.alignment, provides BEASTInterface

     alexeid

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   • Add beagle dependency (optional in beast-base, needed for BeagleTreeLikelihood)

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   • Migrate MutableAlignment to Maven build targeting BEAST3

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     alexeid

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8. Commits on Mar 15, 2026

   • Merge pull request #6 from alexeid/fix-memory-leak

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     rbouckaert

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9. Commits on Mar 8, 2026

   • update BEAST version

     yaox1818

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10. Commits on Mar 6, 2026

    • cache arrays in hot paths to fix memory leak with BEAGLE

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      alexeid

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11. Commits on Dec 8, 2025

    • debugging BeagleMATreeLikelihood

      rbouckaert

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12. Commits on Oct 29, 2025

    • more Beagle stuff

      rbouckaert

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    • start Beagle version of MATreeLikelihood

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13. Commits on Jun 25, 2025

    • do not order taxon by names #4

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14. Commits on Jun 11, 2025

    • fix tests

      rbouckaert

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15. Commits on Jun 10, 2025

    • fix for MATreeLikelihood.getLogProbsForStateSequence()

      rbouckaert

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    • work on cache management

      rbouckaert

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16. Commits on Jun 4, 2025

    • update version number

      yaox1818

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17. Commits on May 29, 2025

    • add getLogProbsForStateSequence() method to MATreeLikelihood

      rbouckaert

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18. Commits on Mar 25, 2025

    • modify initAndValidate function

      yaox1818

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19. Commits on Mar 23, 2025

    • implement resume functionality

      rbouckaert

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20. Commits on Mar 20, 2025

    • update MATreeLikelihood properly after operator. fixes #3

      rbouckaert

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    • add c'tor to MutableAlignment and make it interface. fixes #2

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    • add MutableAlignmentLogger

      rbouckaert

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    • Create operator for MutableAlignment #1

      yaox1818

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21. Commits on Mar 9, 2025

    • fix Edit item creation

      rbouckaert

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