Colgen - Collective Genealogies Visualisation and Analysis

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.