Ancestree 
ancestree is a package for likelihood-based, per-site ancestral-allele annotation, unifying outgroup-based (EST-SFS-style) and ARG-based (PolarBEAR-style) inference behind a single likelihood kernel. It runs in three modes: fixed-tree, ARG, and local-tree, the last inferring its own local genealogies from the variant data rather than taking a supplied ARG. Every site receives a full posterior over the four nucleotide states, with multi-allelic sites, missing data and recurrent mutation handled natively.
Please see the documentation for all the details.
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