Release 4.0-alpha5

This alpha release does not have many user-visible changes, except for a new RNA editing model.

Release 4.0-alpha4

This alpha release does not have many user-visible changes, except for a fix to the mixture distribution.

• Fix alignment_slice_sample_branch_length
• Type system
  • Implement kind inference
  • Create Haskell AST structs
  • Remove struct AST_node
  • Clean up the renamer pass.
  • Refactor Module::compile( )
• Refactor log_double_t
• Add builtins for expm1 and logp1
• Fix mixture distribution
• Make test take input file as a command line argument.
• Refactor the simplier to work better.
• Make generated Haskell code less verbose.

Release 3.6.1

• fix a crash in BES.
• fix mixture distribution
• fix documentation for m8 and m8a models.
• add documentation for m8a_test model.

Release 4.0-alpha3

• Make tree/alignment estimation work on Haskell models.
• Create a dynamic factor graph in addition to the execution dependency graph.

Release 4.0-alpha2

This represents about 3 months of accumulated changes.

• Preliminary relaxed-clock trees.
• Simplify the Haskell modelling language.
• Create a dynamic factor graph and record properties on it.
• Simplify BAli-Phy.Main.hs generated from the command-line.
• Fix --print.
• Fix and update documentation for m8, m8a, and m8a_test.
• Type system: sort declarations into groups, in preparation for kind inference / kind checking.
• Type system: parse and load type classes and instances.
• Parser: create AST objects instead of treating everything as an s-expression
• Parser: print line numbers for undeclared variables.

Release 4.0-alpha1

Preliminary release of the 4.0 branch, to allow running some of the graphical-models code.

Release 3.6.0

Update doc to version 3.6.0

Release 3.5.99

This is beta release is a preview of the forthcoming 3.6.0