Issues

• Migration to beast 3

  enhancement
  bioDS/beast-phylonco#125 · Filter by author kche309 opened on May 18, 2026
  5

• SMC sampler as follow-up to DataTemperedMCMC

  bioDS/beast-phylonco#121 · Filter by author alexeid opened on Mar 6, 2026
  

• Running NestedBD from phylonco project

  documentation
  bioDS/beast-phylonco#117 · Filter by author kche309 opened on Feb 13, 2026
  1

• Allow GT16 substitution and error models to handle NucleotideDiploid10 data

  enhancement
  bioDS/beast-phylonco#105 · Filter by author kche309 opened on Oct 16, 2025
  

• Implement GT10 error model

  enhancement
  bioDS/beast-phylonco#104 · Filter by author kche309 opened on Oct 16, 2025

• Review lphy datatype naming, error message: Unphased genotype not supported for error model.

  bugmethod naming
  bioDS/beast-phylonco#98 · Filter by author EvaLiyt opened on Sep 30, 2025
  3

• [Beast Junit] Junit tests using NucleotideDiploid16 data type cannot be initialized

  bug
  bioDS/beast-phylonco#95 · Filter by author kche309 opened on Sep 22, 2025
  1

• [Beast Junit] Unable to find beast jar for Junit tests

  bug
  bioDS/beast-phylonco#94 · Filter by author kche309 opened on Sep 22, 2025
  

• [LphyBeast] Missing integration test for unphase function

  bioDS/beast-phylonco#93 · Filter by author kche309 opened on Sep 22, 2025
  2

  

• [LPhy Junit] Unit tests in NucleotideGenotypeHelperTest failing

  bug
  bioDS/beast-phylonco#92 · Filter by author kche309 opened on Sep 22, 2025
  1

  

• Developer guidelines and rules

  Developer Rules
  bioDS/beast-phylonco#87 · Filter by author kche309 opened on Aug 28, 2025
  2

• Make version numbers updatable from a single location

  documentationenhancementhelp wanted
  bioDS/beast-phylonco#86 · Filter by author kche309 opened on Aug 28, 2025

• Running beast from IntelliJ without MutableAlignment package install causes issues

  bug
  bioDS/beast-phylonco#84 · Filter by author kche309 opened on Aug 28, 2025
  

• Release 1.2.1

  bioDS/beast-phylonco#69 · Filter by author walterxie opened on Oct 30, 2024

• LPhy Studio freezes when resampling some scripts

  bug
  bioDS/beast-phylonco#68 · Filter by author kche309 opened on Oct 3, 2024

• Version management for dependencies: add "atmost="

  enhancement
  bioDS/beast-phylonco#67 · Filter by author walterxie opened on Sep 30, 2024

• Implement stochastic variable selection for population functions

  bioDS/beast-phylonco#64 · Filter by author yxu927 opened on Jul 16, 2024

• Get warnings when running lphy scripts

  enhancement
  bioDS/beast-phylonco#59 · Filter by author yxu927 opened on May 13, 2024

• Add Viewer for read count data in LPhyStudio

  enhancement
  bioDS/beast-phylonco#58 · Filter by author kche309 opened on May 6, 2024

• Implement read count model for LPhy simulation

  enhancement
  bioDS/beast-phylonco#56 · Filter by author kche309 opened on Apr 18, 2024

• LPhyBeast for gompertz model

  enhancement
  bioDS/beast-phylonco#55 · Filter by author yxu927 opened on Apr 15, 2024

• Create API class to define the mapping between PhasedGenotypeState and NucleotideState

  enhancement
  bioDS/beast-phylonco#48 · Filter by author walterxie opened on Feb 19, 2024

• Question Regarding Effective Population Size

  bioDS/beast-phylonco#36 · Filter by author SriRaj34 opened on Dec 5, 2022
  2

• Port PMD error model from BEAST1

  enhancement
  bioDS/beast-phylonco#22 · Filter by author kche309 opened on Mar 1, 2022
  3

• Beauti templates for substitution models

  enhancement
  bioDS/beast-phylonco#10 · Filter by author kche309 opened on Jan 28, 2022
  1