Issues

• Replace unwrap_or_else(|e| bug!("msg", e)); with unwrap_or_bug("msg")

  enhancement
  Feature

  acg-team/phyne#209 · Filter by author MattesMrzik opened on Oct 28, 2026

• Consistent names for ASR / Homology Path Inference Structs

  acg-team/phyne#205 · Filter by author MattesMrzik opened on Oct 23, 2026

• Substitution models and PIP should check that parameters are non-negative and finite

  bug
  Bug

  acg-team/phyne#204 · Filter by author junniest opened on Oct 23, 2026
  

• Tree internal node traversal

  acg-team/phyne#203 · Filter by author MattesMrzik opened on Oct 23, 2026

• Add comments to bail in macros and error.rs

  documentation
  acg-team/phyne#202 · Filter by author MattesMrzik opened on Oct 21, 2026
  

• Add Alignment::is_empty() and AncestralAlignment::is_empty() to traits

  enhancement
  acg-team/phyne#199 · Filter by author junniest opened on Oct 20, 2026

• Tree pruning without serialization

  question
  acg-team/phyne#198 · Filter by author MattesMrzik opened on Oct 19, 2026
  1

• PhyloInfo fns for both A and AA

  acg-team/phyne#197 · Filter by author MattesMrzik opened on Oct 16, 2026

• Calling ModelOptimiser on JC69/K80 with FrequencyOptimisation::Empirical fails

  enhancement
  Feature

  acg-team/phyne#194 · Filter by author junniest opened on Oct 6, 2026

• Evolutionary models should bail on incorrect parameters

  enhancement
  Feature

  acg-team/phyne#193 · Filter by author junniest opened on Oct 6, 2026
  1

  

• Refactor Alignment

  acg-team/phyne#190 · Filter by author MattesMrzik opened on Sep 28, 2026
  2

• ASR with TKF needs optimization hyper parameters

  questionTKF
  acg-team/phyne#189 · Filter by author MattesMrzik opened on Sep 26, 2026
  1

• Tree and LabeledTree trait

  acg-team/phyne#188 · Filter by author MattesMrzik opened on Sep 23, 2026
  1

• Internal node IDs should be also checked for duplicates (if provided)

  bug
  Bug

  acg-team/phyne#187 · Filter by author junniest opened on Sep 18, 2026
  2

  

• NJTreeBuilder::build_from_distances() should not require the sequences as input

  refactor me
  Task

  acg-team/phyne#186 · Filter by author junniest opened on Sep 18, 2026
  

• Parsimony aligner should not use Sequences::with_alphabet_unchecked() and A::from_aligned_unchecked()

  acg-team/phyne#183 · Filter by author junniest opened on Sep 14, 2026
  

• PairwiseAlignment::new() should bail and not panic

  acg-team/phyne#182 · Filter by author junniest opened on Sep 10, 2026

• Clean up public API

  acg-team/phyne#181 · Filter by author junniest opened on Sep 10, 2026
  

• Complete documentation at crate level

  acg-team/phyne#180 · Filter by author junniest opened on Sep 9, 2026
  

• trait method param_name for cost?

  question
  acg-team/phyne#176 · Filter by author MattesMrzik opened on Jun 25, 2026

• Recover bits of precision in TKF92 block prob

  enhancementTKF
  acg-team/phyne#174 · Filter by author MattesMrzik opened on Apr 17, 2026

• TKF EdgeSeqsReestimator without mut ref?

  questionTKF
  acg-team/phyne#172 · Filter by author MattesMrzik opened on Apr 16, 2026

• Add file paths to io errors

  enhancement
  Feature

  acg-team/phyne#169 · Filter by author MattesMrzik opened on Mar 27, 2026
  

• Streamline TKF simulation

  TKF
  acg-team/phyne#163 · Filter by author MattesMrzik opened on Mar 25, 2026

• Host docs for crate

  documentation
  Feature

  acg-team/phyne#161 · Filter by author junniest opened on Mar 11, 2026