Comparison of orchard networks using their extended μ-representation
G Cardona, JC Pons, G Ribas… - IEEE/ACM Transactions …, 2024 - ieeexplore.ieee.org
Phylogenetic networks generalize phylogenetic trees in order to model reticulation events.
Although the comparison of phylogenetic trees is well studied, and there are multiple ways …
Although the comparison of phylogenetic trees is well studied, and there are multiple ways …
Inference of phylogenetic networks from sequence data using composite likelihood
While phylogenies have been essential in understanding how species evolve, they do not
adequately describe some evolutionary processes. For instance, hybridization, a common …
adequately describe some evolutionary processes. For instance, hybridization, a common …
Recent progress on methods for estimating and updating large phylogenies
P Zaharias, T Warnow - Philosophical Transactions of the …, 2022 - royalsocietypublishing.org
With the increased availability of sequence data and even of fully sequenced and
assembled genomes, phylogeny estimation of very large trees (even of hundreds of …
assembled genomes, phylogeny estimation of very large trees (even of hundreds of …
Clustering systems of phylogenetic networks
Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set X of taxa
involves not only speciations but also recombination, horizontal transfer, or hybridization that …
involves not only speciations but also recombination, horizontal transfer, or hybridization that …
Practical guidelines for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC)
J Barido-Sottani, O Schwery… - Open Research …, 2024 - pmc.ncbi.nlm.nih.gov
Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a
phylogenetic tree involves evaluating many possible solutions and possible evolutionary …
phylogenetic tree involves evaluating many possible solutions and possible evolutionary …
A 2-approximation algorithm for the softwired parsimony problem on binary, tree-child phylogenetic networks
M Frohn, S Kelk - arXiv preprint arXiv:2409.18077, 2024 - arxiv.org
Finding the most parsimonious tree inside a phylogenetic network with respect to a given
character is an NP-hard combinatorial optimization problem that for many network …
character is an NP-hard combinatorial optimization problem that for many network …
Mathematically tractable models of random phylogenetic networks: an overview of some recent developments
F Bienvenu - arXiv preprint arXiv:2410.13574, 2024 - arxiv.org
Models of random phylogenetic networks have been used since the inception of the field,
but the introduction and rigorous study of mathematically tractable models is a much more …
but the introduction and rigorous study of mathematically tractable models is a much more …
Transformations to simplify phylogenetic networks
The evolutionary relationships between species are typically represented in the biological
literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate …
literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate …
Statistical learning with phylogenetic network invariants
Phylogenetic networks provide a means of describing the evolutionary history of sets of
species believed to have undergone hybridization or gene flow during their evolution. The …
species believed to have undergone hybridization or gene flow during their evolution. The …
Labellable phylogenetic networks
Phylogenetic networks are mathematical representations of evolutionary history that are
able to capture both tree-like evolutionary processes (speciations) and non-tree-like …
able to capture both tree-like evolutionary processes (speciations) and non-tree-like …