Issues

• Substitution models allow to set negative frequencies

  bug
  Bug

  acg-team/phyne#191 · Filter by author junniest opened on Sep 29, 2026
  

• 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
  1

  

• 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
  

• Should MSAs and MASAs be built as PhyloInfo?

  question
  Feature

  acg-team/phyne#184 · Filter by author junniest opened on Sep 16, 2026
  1

  

• 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

• TKF Reestimate numerical differences: dp logl and tree.postorder logl

  enhancementTKF
  Bug

  acg-team/phyne#175 · Filter by author MattesMrzik opened on May 19, 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
  

• Crate rename

  enhancement
  Task

  acg-team/phyne#160 · Filter by author junniest opened on Mar 10, 2026 · 1.0.0 release
  1

  

• git hub action and badge for MSRV?

  question
  Feature

  acg-team/phyne#156 · Filter by author MattesMrzik opened on Feb 24, 2026
  1

• errors instead of panics

  enhancement
  Task

  acg-team/phyne#155 · Filter by author MattesMrzik opened on Feb 24, 2026
  1

• Update blocks upon ancestral wild card re-estimation

  bugTKF
  Bug

  acg-team/phyne#154 · Filter by author MattesMrzik opened on Feb 5, 2026

• Speed up TKF cost

  enhancementTKF
  Task

  acg-team/phyne#152 · Filter by author MattesMrzik opened on Feb 3, 2026

• Speed up TKF ancestral reestimation

  enhancementTKF
  Task

  acg-team/phyne#151 · Filter by author MattesMrzik opened on Feb 3, 2026
  2

• Realignment and internal maps for TKF

  enhancementTKF
  Feature

  acg-team/phyne#150 · Filter by author MattesMrzik opened on Feb 3, 2026