18 citations · 23 across the 6 of their papers we have counts for
8 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…