71 citations · 78 across the 5 of their papers we have counts for
6 papers
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…
Lie-Markov models derived from finite semigroups
Jeremy G. Sumner, Michael D. Woodhams
We present and explore a general method for deriving a Lie-Markov model from a finite semigroup. If the degree of the semigroup is , the resulting model is a continuous-time Mar…
A new hierarchy of phylogenetic models consistent with heterogeneous substitution rates
Michael D. Woodhams, Jesús Fernández-Sánchez, Jeremy G. Sumner
When the process underlying DNA substitutions varies across evolutionary history, the standard Markov models underlying standard phylogenetic methods are mathematically inconsisten…
Lie Markov models with purine/pyrimidine symmetry
Jesús Fernández-Sánchez, Jeremy G. Sumner, Peter D. Jarvis +1
Continuous-time Markov chains are a standard tool in phylogenetic inference. If homogeneity is assumed, the chain is formulated by specifying time-independent rates of substitution…
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…