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Performance-based selection of likelihood models for phylogeny estimation.
Phylogenetic estimation has largely come to rely on explicitly model-based methods. This approach requires that a model be chosen and that that choice be justified. To date, justification has largely… Expand
Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics.
Kingman's coalescent process opens the door for estimation of population genetics model parameters from molecular sequences. One paramount parameter of interest is the effective population size.… Expand
Species delimitation using genome-wide SNP data.
The multispecies coalescent has provided important progress for evolutionary inferences, including increasing the statistical rigor and objectivity of comparisons among competing species delimitation… Expand
Species Delimitation using Genome-Wide SNP Data
We combine a recently introduced dynamic programming algorithm for estimating species trees that bypasses MCMC integration over gene trees with sophisticated methods for estimating marginal likelihoods, needed for Bayesian model selection, to provide a rigorous and computationally tractable technique for genome-wide species delimitation. Expand
Dual multiple change-point model leads to more accurate recombination detection
MOTIVATION We introduce a dual multiple change-point (MCP) model for recombination detection among aligned nucleotide sequences. Expand
Fast, accurate and simulation-free stochastic mapping
- V. Minin, M. Suchard
- Biology, Medicine
- Philosophical Transactions of the Royal Society B…
- 27 December 2008
Mapping evolutionary trajectories of discrete traits onto phylogenies receives considerable attention in evolutionary biology. Given the trait observations at the tips of a phylogenetic tree,… Expand
Learning to count: robust estimates for labeled distances between molecular sequences.
Researchers routinely estimate distances between molecular sequences using continuous-time Markov chain models. We present a new method, robust counting, that protects against the possibly severe… Expand
Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).
The anomaly zone, defined by the presence of gene tree topologies that are more probable than the true species tree, presents a major challenge to the accurate resolution of many parts of the Tree of… Expand
Counting labeled transitions in continuous-time Markov models of evolution
Counting processes that keep track of labeled changes to discrete evolutionary traits play critical roles in evolutionary hypothesis testing. If we assume that trait evolution can be described by a… Expand
A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection
- P. Lemey, V. Minin, Filip Bielejec, S. Pond, M. Suchard
- Biology, Computer Science
- 1 November 2012
We propose a hybrid solution that borrows the computational strength of counting methods, but augments these methods with empirical Bayes modeling to produce a relatively fast and reliable method capable of estimating site-specific dN/dS values in large datasets. Expand