4.0-beta17

This release speeds up likelihood calculations and adds some new codon models.

• Speed:
  • Use sparse likelihood vectors for leaf branches.
  • Use faster eigenvalue method to compute exp(Q*t) by default, falling back to slower method if needed.
• Models:
  • Multi-Nucleotide-Mutation (MNM) model for codons.
  • BUSTED and BUSTED-S substitution models for positive selection.
  • Initial cmdline version of multi_freq model.
• Bug fixes:
  • Sort the logged dN/dS values for m3_test
• Haskell:
  • Implement strict fields for data types with !type.
  • Improved error messages for type errors.