31 citations · 93 across the 27 of their papers we have counts for
36 papers
Binary normal networks without near reticulations can be reconstructed from their rooted triples
Andrew Francis, Charles Semple
Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While too…
Counting spinal phylogenetic networks
Andrew Francis, Michael Hendriksen
Phylogenetic networks are an important way to represent evolutionary histories that involve reticulations such as hybridization or horizontal gene transfer, yet fundamental questio…
Factorizing the Brauer monoid in polynomial time
Daniele Marchei, Emanuela Merelli, Andrew Francis
Finding a minimal factorization for a generic semigroup can be done by using the Froidure-Pin Algorithm, which is not feasible for semigroups of large sizes. On the other hand, if…
Phylogenetic network classes through the lens of expanding covers
Andrew Francis, Daniele Marchei, Mike Steel
It was recently shown that a large class of phylogenetic networks, the `labellable' networks, is in bijection with the set of `expanding' covers of finite sets. In this paper, we s…
An algebraic model for inversion and deletion in bacterial genome rearrangement
Chad Clark, Julius Jonušas, James D. Mitchell +1
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are…
A polynomial invariant for a new class of phylogenetic networks
Joan Carles Pons, Tomás M. Coronado, Michael Hendriksen +1
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important too…
Brauer and partition diagram models for phylogenetic trees and forests
Andrew Francis, Peter D Jarvis
We introduce a correspondence between phylogenetic trees and Brauer diagrams, inspired by links between binary trees and matchings described by Diaconis and Holmes (1998). This cor…
Encoding and ordering X-cactuses
Andrew Francis, Katharina T. Huber, Vincent Moulton +1
Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another. A specia…
"Normal" phylogenetic networks may be emerging as the leading class
Andrew Francis
The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with bio…
Phylogenetic Diversity Rankings in the Face of Extinctions: the Robustness of the Fair Proportion Index
Mareike Fischer, Andrew Francis, Kristina Wicke
Planning for the protection of species often involves difficult choices about which species to prioritize, given constrained resources. One way of prioritizing species is to consid…
A path-deformation framework for determining weighted genome rearrangement distance
Sangeeta Bhatia, Attila Egri-Nagy, Stuart Serdoz +3
Measuring the distance between two bacterial genomes under the inversion process is usually done by assuming all inversions to occur with equal probability. Recently, an approach t…
Normalising phylogenetic networks
Andrew Francis, Daniel H. Huson, Mike Steel
Rooted phylogenetic networks provide a way to describe species' relationships when evolution departs from the simple model of a tree. However, networks inferred from genomic data c…
Rooted NNI moves on tree-based phylogenetic networks
Péter L. Erdős, Andrew Francis, Tamás Róbert Mezei
We show that the space of rooted tree-based phylogenetic networks is connected under rooted nearest-neighbour interchange (rNNI) moves.
The space of tree-based phylogenetic networks
Mareike Fischer, Andrew Francis
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also…
Tree-metrizable HGT networks
Michael Hendriksen, Andrew Francis
Phylogenetic trees are often constructed by using a metric on the set of taxa that label the leaves of the tree. While there are a number of methods for constructing a tree using a…
How tree-based is my network? Proximity measures for unrooted phylogenetic networks
Mareike Fischer, Andrew Francis
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, howev…
A partial order and cluster-similarity metric on rooted phylogenetic trees
Michael Hendriksen, Andrew Francis
Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in…
A mean first passage time genome rearrangement distance
Andrew Francis, Henry Wynn
This paper introduces a new way to define a genome rearrangement distance, using the concept of mean first passage time from probability theory. Crucially, this distance estimate p…
Lattice consensus: A partial order on phylogenetic trees that induces an associatively stable consensus method
Michael Hendriksen, Andrew Francis
There is a long tradition of the axiomatic study of consensus methods in phylogenetics that satisfy certain desirable properties. One recently-introduced property is associative st…
Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution
Andrew Francis, Vincent Moulton
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridizatio…
Inferences on the acquisition of multidrug resistance in \emph{Mycobacterium tuberculosis} using molecular epidemiological data
Guilherme S. Rodrigues, Andrew R. Francis, Scott A. Sisson +1
We investigate the rates of drug resistance acquisition in a natural population using molecular epidemiological data from Bolivia. First, we study the rate of direct acquisition of…
Tree-based unrooted phylogenetic networks
Andrew Francis, Katharina Huber, Vincent Moulton
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria…
Bounds for phylogenetic network space metrics
Andrew Francis, Katharina Huber, Vincent Moulton +1
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was intr…
A representation-theoretic approach to the calculation of evolutionary distance in bacteria
Jeremy G Sumner, Peter D Jarvis, Andrew R Francis
In the context of bacteria and models of their evolution under genome rearrangement, we explore a novel application of group representation theory to the inference of evolutionary…