phylox.cherrypicking

A module for constructing and reducing networks using cherry-picking.

This code was initially based on a collection of scripts used for several papers:

• “On cherry-picking and network containment” by Remie Janssen and Yukihiro Murakami (2020)

• “Combining networks using cherry picking sequences” by Remie Janssen, Mark Jones, and Yukihiro Murakami (2020)

• “Linear Time Algorithm for Tree-Child network Containment” by Remie Janssen and Yukihiro Murakami (2020)

• “A practical fixed-parameter algorithm for constructing tree-child networks from multiple binary trees” by Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami, and Norbert Zeh (2022)

and some unpublished work that was continued by Esther Julien:

• Constructing Phylogenetic Networks via Cherry Picking and Machine Learning” by G BErnardini, LJJ van Iersel, E Julien, and L Stougie (2023)

Modules

phylox.cherrypicking.Heuristic_Main_UserFriendly
phylox.cherrypicking.base
phylox.cherrypicking.best_subnetwork
phylox.cherrypicking.combining_networks
phylox.cherrypicking.tree_child_sequences	Functions for finding tree child sequences in a network.