phylox.generators.lgt.base

A module for generating (random) LGT phylogenetic networks.

By Joan Carles Pons, Celine Scornavacca, Gabriel Cardona With their paper: Generation of Level-k LGT Networks PMID: 30703035 DOI: 10.1109/TCBB.2019.2895344

Adapted by RemieJanssen to output networks with a given number of leaves and reticulations

Functions

compute_hash(net)
internal_and_external_pairs(net)
internal_blobs(net)
last_node(net)
leaves(net)
lgt(net, leaf1, leaf2)
reticulations(G)
speciate(net, leaf)

phylox.generators.lgt.base.simulation_3(leaves_goal, retics_goal, wint, wext, seed=None)

Simulation 3 for generating networks with a given number of leaves and reticulations :param leaves_goal: number of leaves in the network :param retics_goal: number of reticulations in the network :param wint: weight of internal edges :param wext: weight of external edges :return: a network with the given number of leaves and reticulations

phylox.generators.lgt.base.generate_network_lgt(n, k, wint=1, wext=1, max_tries=1000, seed=None)

Generate a network with a given number of leaves and reticulations :param n: number of leaves :param k: number of reticulations :param alpha: parameter for the weight of internal edges :param beta: parameter for the weight of external edges :param max_tries: maximum number of tries to generate a network :param seed: seed for the random number generator :return: a network with the given number of leaves and reticulations