v4.0.0

Summary

• A major enhancement for parsimony tree search is the use of a history DAG to expand the set of trees found by dnapars, often by orders of magnitude. h/t @willdumm
• Tree ranking can now use a linear combination of branching process likelihood, isotype parsimony, and mutability parsimony (e.g. from a 5mer context model) to score trees.

Backwards-incompatible changes

• The CollapsedForest class no longer has a trees attribute, as the collection of trees is now represented as a history DAG.
• The gctree CLI can now accept pickled parsimony forests from the current gctree version, but not from older versions.
• Only the unique optimal tree is output by gctree infer, if it exists. If more than one tree is optimal, up to 10 will be output arbitrarily, and their numerical rankings will be arbitrary (rather than based on likelihood as before).

Pull requests

• Fit parameters on history DAG by @willdumm in #68
• Add ambiguous sequence test and error message by @willdumm in #72
• Transplant docs by @wsdewitt in #73
• Transplant patch by @wsdewitt in #74
• Docs fixes by @wsdewitt in #76
• Update README.md by @wsdewitt in #77
• Store isotype data in nodes by @willdumm in #75
• Mutability chain split by @willdumm in #78
• Prerelease tidying by @wsdewitt in #79

Full Changelog: v3.3.0...v4.0.0