Colgen is a python package to visualise and analyse collective-level genealogies. Its features include: - Visualise propagation-replacement data in the form of a tree where each node correspond to a collective, interactively (served locally as HTML) or statically (using the python API). - Build a Binary Bayesian Network representation of the genealogy where each node display (1) or not (0) a mutation. Use a Maximum-a-posteriori method to infer probable the location of mutations in the genealogy (from a few sequenced points). - Build a Continuous Bayesian Network representation of the genealogy where each node is associated with a survival probability. Use a Maximum-a-posteriori method to infer locations in the genealogy where this probability changes. For more information see the readme file. Development is ongoing.

Colgen was first released as part of Guilhem Doulcier's PhD thesis (https://pastel.archives-ouvertes.fr/tel-02917058)