Despite the inherently fuzzy nature of reconstructions in historical linguistics, most scholars do not represent their uncertainty when proposing proto-forms. With the increasing success of recently proposed approaches to automating certain aspects of the traditional comparative method, the formal representation of proto-forms has also improved. This formalization makes it possible to address both the representation and the computation of uncertainty. Building on recent advances in supervised phonological reconstruction, during which an algorithm learns how to reconstruct words in a given proto-language relying on previously annotated data, and inspired by improved methods for automated word prediction from cognate sets, we present a new framework that allows for the representation of uncertainty in linguistic reconstruction and also includes a workflow for the computation of fuzzy reconstructions from linguistic data.