BAli---Phy

Release Notes

See the NEWS file for more information.

• Speed & Memory
  • Memory: Fix excess memory usage on large trees in 3.5-3.6
• Models
  • Codon models:
    • BUSTED and BUSTED-S model
    • Multi-nucleotide mutation (MNM) models
    • Non-standard genetic codes
  • Modeling language:
    • See Probabilistic Programming language
  • Non-reversible and non-equilibrium substitution models
  • Relaxed rates
    • Branch-specific insertion-deletion rates.