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 atrees
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