new features - Githubissues

harmslab / topiary

Python framework for doing ancestral sequence reconstruction

MIT License

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new features #17

Closed harmsm closed 1 year ago

harmsm commented 1 year ago

Implemented most new features for ms revision/initial release of topiary.

Generates html reports
Chooses whether to reconcile gene/species trees based on species distribution
Chooses how to lower redundancy based on species distribution
Fixed bug in redundancy reduction code that caused reduction-by-identity to silently fail.

Still to-do:

Better testing framework for new features
Have pipelines spit out ML ancestors
Allow species without OTT if not planning to do reconciliation