1 code implementation • 11 May 2024 • Cedric Chauve, Caroline Colijn, Louxin Zhang
The HOP distance can be computed in near-linear time, a rare instance of a tree rearrangement distance that is tractable.
no code implementations • 30 Nov 2023 • Yufeng Wu, Louxin Zhang
Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e. g., hybrid speciation or horizontal gene transfer) occurred.
no code implementations • 14 Jan 2023 • Elahe Khayatian, Gabriel Valiente, Louxin Zhang
Like the Robinson-Foulds distance, the k-Robinson-Foulds is a pseudometric for multiset-labeled trees and becomes a metric in the space of 1-labeled trees.
no code implementations • 3 Jan 2023 • Louxin Zhang, Niloufar Abhari, Caroline Colijn, Yufeng Wu
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well.
no code implementations • 6 Jul 2022 • Yufeng Wu, Louxin Zhang
It is also proved that any set of multiple binary phylogenetic trees can always simultaneously be displayed in some non-binary tree-child network on the same taxa set, where each nonleaf node is of either indegree one and outdegree two or indegree at least two and outdegree out.
no code implementations • 26 Jan 2022 • Gary Goh, Michael Fuchs, Louxin Zhang
Another is a short elementary proof of the closed formula for the expected Sackin index of phylogenetic trees (which are full binary rooted trees with leaves being labelled with taxa) under the uniform model.
no code implementations • 31 Dec 2021 • Louxin Zhang
A phylogenetic network is a simplex (or 1-component tree-child) network if the child of every reticulation node is a network leaf.
no code implementations • 20 Dec 2018 • Andreas DM Gunawan, Jeyaram Rathin, Louxin Zhang
Galled trees are widely studied as a recombination model in population genetics.
Populations and Evolution
1 code implementation • 5 Sep 2015 • Louxin Zhang
Reticulation-visible networks and child-sibling networks are all tree based.
