Issues

• Understand the gaps between lphy and phylospec

  LinguaPhylo/linguaPhylo#578 · Filter by author walterxie opened on Aug 27, 2026 · 2.0

• PhyloSpec -> lphy2

  LinguaPhylo/linguaPhylo#577 · Filter by author walterxie opened on Aug 27, 2026 · 2.0
  1

• Add a FossilizedCPP distribution for FBD inference on dated tip alignments

  LinguaPhylo/linguaPhylo#574 · Filter by author alexeid opened on May 8, 2026

• Moving towards to LPhy 2 : adapt to Phylospec

  critical change
  LinguaPhylo/linguaPhylo#561 · Filter by author walterxie opened on Aug 12, 2025 · 2.0

• h5n1BDSS example randomly fail

  LinguaPhylo/linguaPhylo#560 · Filter by author EvaLiyt opened on Aug 7, 2025
  1

• LPhy Studio window freezes when sampling a large tree and alignment

  bug
  LinguaPhylo/linguaPhylo#547 · Filter by author kche309 opened on May 1, 2025

• Unified framework for discrete and continuous evolution models

  critical change
  LinguaPhylo/linguaPhylo#544 · Filter by author alexeid opened on Apr 1, 2025

• New PhyloCTMC to simulate sequences by sampling mutations through the tree

  enhancement
  LinguaPhylo/linguaPhylo#538 · Filter by author walterxie opened on Mar 11, 2025

• Fix parent version in pom

  enhancement
  LinguaPhylo/linguaPhylo#535 · Filter by author walterxie opened on Oct 24, 2024
  1

• Setup Maven repository in Github

  critical changeenhancement
  LinguaPhylo/linguaPhylo#516 · Filter by author walterxie opened on Aug 14, 2024
  1

• Improve Maven test for multiple projects

  enhancement
  LinguaPhylo/linguaPhylo#513 · Filter by author walterxie opened on Aug 6, 2024
  1

• Log variables not being saved correctly

  LinguaPhylo/linguaPhylo#509 · Filter by author yaox1818 opened on Jul 28, 2024
  4

• Need validation to all GenerativeDistribution and Function implemented correctly

  enhancementlong term
  LinguaPhylo/linguaPhylo#502 · Filter by author walterxie opened on Jul 4, 2024

• implement CalibratedYule distribution

  enhancement
  LinguaPhylo/linguaPhylo#497 · Filter by author EvaLiyt opened on Jun 18, 2024
  2

• Aged conditional coalescent

  enhancement
  LinguaPhylo/linguaPhylo#487 · Filter by author walterxie opened on Jun 5, 2024

• Allow replicates to be a vector

  critical changeenhancement
  LinguaPhylo/linguaPhylo#486 · Filter by author walterxie opened on Jun 5, 2024

• unnecessary logging

  enhancement
  LinguaPhylo/linguaPhylo#484 · Filter by author walterxie opened on Jun 4, 2024

• Why we need BasicFunction?

  question
  LinguaPhylo/linguaPhylo#480 · Filter by author walterxie opened on May 23, 2024
  2

• Add ProgressBar

  enhancement
  LinguaPhylo/linguaPhylo#474 · Filter by author walterxie opened on May 15, 2024

• Add memory efficient version of ErrorAlignment

  enhancement
  LinguaPhylo/linguaPhylo#466 · Filter by author kche309 opened on May 6, 2024

• Implement Multinomial distribution

  enhancement
  LinguaPhylo/linguaPhylo#463 · Filter by author kche309 opened on Apr 18, 2024

• merge PopulationFunctionCoalescent to SerialCoalescent

  enhancement
  LinguaPhylo/linguaPhylo#462 · Filter by author walterxie opened on Apr 17, 2024

• Simplify the SPI framework in lphy

  critical changeenhancement
  LinguaPhylo/linguaPhylo#454 · Filter by author walterxie opened on Apr 4, 2024
  1

• Implement Ascertainment Corrections

  LinguaPhylo/linguaPhylo#450 · Filter by author SimonGreenhill opened on Mar 4, 2024
  2

• Create new lphy extension to use beast2 nexus parser

  enhancement
  LinguaPhylo/linguaPhylo#446 · Filter by author walterxie opened on Feb 7, 2024
  1