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Charnet

Computes the trees, tripartitions and clusters contained in a phylogenetic network.

Cmpnets

Computes the distance between two phylogenetic networks based on their topologies.

CountCoal

Ccomputes Computes the number of coalescent scenarios that can explain the incongruence observed between two trees.

DeepCoalCount

Count the number of extra lineages contributed by a species tree and a set of gene trees.