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Migration to beast 3

enhancementNew feature or requestNew feature or request

Status: Open.

#125 In bioDS/beast-phylonco;

· kche309 opened on May 18, 2026

SMC sampler as follow-up to DataTemperedMCMC

Status: Open.

#121 In bioDS/beast-phylonco;

· alexeid opened on Mar 6, 2026

Running NestedBD from phylonco project

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#117 In bioDS/beast-phylonco;

· kche309 opened on Feb 13, 2026

Allow GT16 substitution and error models to handle NucleotideDiploid10 data

enhancementNew feature or requestNew feature or request

Status: Open.

#105 In bioDS/beast-phylonco;

· kche309 opened on Oct 16, 2025

Implement GT10 error model

enhancementNew feature or requestNew feature or request

Status: Open.

#104 In bioDS/beast-phylonco;

· kche309 opened on Oct 16, 2025

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

bugSomething isn't workingSomething isn't working

method naming

Status: Open.

#98 In bioDS/beast-phylonco;

· EvaLiyt opened on Sep 30, 2025

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

bugSomething isn't workingSomething isn't working

Status: Open.

#95 In bioDS/beast-phylonco;

· kche309 opened on Sep 22, 2025

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

bugSomething isn't workingSomething isn't working

Status: Open.

#94 In bioDS/beast-phylonco;

· kche309 opened on Sep 22, 2025

[LphyBeast] Missing integration test for unphase function

Status: Open.

#93 In bioDS/beast-phylonco;

· kche309 opened on Sep 22, 2025

[LPhy Junit] Unit tests in NucleotideGenotypeHelperTest failing

bugSomething isn't workingSomething isn't working

Status: Open.

#92 In bioDS/beast-phylonco;

· kche309 opened on Sep 22, 2025

Developer guidelines and rules

Developer RulesRules and guidelines for developers.Rules and guidelines for developers.

Status: Open.

#87 In bioDS/beast-phylonco;

· kche309 opened on Aug 28, 2025

Make version numbers updatable from a single location

documentationImprovements or additions to documentationImprovements or additions to documentation

enhancementNew feature or requestNew feature or request

help wantedExtra attention is neededExtra attention is needed

Status: Open.

#86 In bioDS/beast-phylonco;

· kche309 opened on Aug 28, 2025