71 citations · 115 across the 14 of their papers we have counts for
15 papers
Evaluation of the relative performance of the subflattenings method for phylogenetic inference
Joshua Stevenson, Barbara Holland, Michael Charleston +1
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern…
The Shape of Phylogenies Under Phase-Type Distributed Times to Speciation and Extinction
Albert Ch. Soewongsono, Barbara R. Holland, Małgorzata M. O'Reilly
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionar…
The ancient Operational Code is embedded in the amino acid substitution matrix and aaRS phylogenies
Julia A. Shore, Barbara R. Holland, Jeremy G. Sumner +2
The underlying structure of the canonical amino acid substitution matrix (aaSM) is examined by considering stepwise improvements in the differential recognition of amino acids acco…
The impracticalities of multiplicatively-closed codon models: a retreat to linear alternatives
Julia A. Shore, Jeremy G. Sumner, Barbara R. Holland
A matrix Lie algebra is a linear space of matrices closed under the operation . The "Lie closure" of a set of matrices is the smallest matrix Lie algebra which co…
Exploring the consequences of lack of closure in codon models
Michael D. Woodhams, Jeremy G. Sumner, David A. Liberles +2
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolution…
Distinguishing between convergent evolution and violation of the molecular clock
Jonathan D. Mitchell, Jeremy G. Sumner, Barbara R. Holland
We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of species post speciation…
Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants
Jeremy G Sumner, Amelia Taylor, Barbara R Holland +1
Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these a…
Comparison of three Statistical Classification Techniques for Maser Identification
Ellen M. Manning, Barbara R. Holland, Simon P. Ellingsen +3
We applied three statistical classification techniques - linear discriminant analysis (LDA), logistic regression and random forests - to three astronomical datasets associated with…
Maximum likelihood estimates of pairwise rearrangement distances
Stuart Serdoz, Attila Egri-Nagy, Jeremy Sumner +4
Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a ra…
Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods
Paul Fearnhead, Shoukai Yu, Patrick Biggs +2
A number of studies have suggested using comparisons between DNA sequences of closely related bacterial isolates to estimate the relative rate of recombination to mutation for that…
A tensorial approach to the inversion of group-based phylogenetic models
Jeremy G. Sumner, Peter D. Jarvis, Barbara R. Holland
Using a tensorial approach, we show how to construct a one-one correspondence between pattern probabilities and edge parameters for any group-based model. This is a generalisation…
Low-parameter phylogenetic estimation under the general Markov model
Barbara R. Holland, Peter D. Jarvis, Jeremy G. Sumner
In their 2008 and 2009 papers, Sumner and colleagues introduced the "squangles" - a small set of Markov invariants for phylogenetic quartets. The squangles are consistent with the…
Novel Distances for Dollo Data
Michael Woodhams, Dorothy A. Steane, Rebecca C. Jones +3
We investigate distances on binary (presence/absence) data in the context of a Dollo process, where a trait can only arise once on a phylogenetic tree but may be lost many times. W…
Is the general time-reversible model bad for molecular phylogenetics?
Jeremy Sumner, Peter Jarvis, Jesus Fernandez-Sanchez +3
The general time reversible model (GTR) is presently the most popular model used in phylogentic studies. However, GTR has an undesirable mathematical property that is potentially o…
The algebra of the general Markov model on phylogenetic trees and networks
J. G. Sumner, B. H. Holland, P. D. Jarvis
It is known that the Kimura 3ST model of sequence evolution on phylogenetic trees can be extended quite naturally to arbitrary split systems. However, this extension relies heavily…