4 papers · 1 filter
A surrogate function for one-dimensional phylogenetic likelihoods
Brian C. Claywell, Vu C. Dinh, Connor O. McCoy +1
Phylogenetics has seen an steady increase in substitution model complexity, which requires increasing amounts of computational power to compute likelihoods. This model complexity m…
Quantifying evolutionary constraints on B cell affinity maturation
Connor O. McCoy, Trevor Bedford, Vladimir N. Minin +3
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain de…
Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth
Connor O. McCoy, Frederick A. Matsen
In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply count-only measures such as Simpson's index to Operat…
Minimizing the average distance to a closest leaf in a phylogenetic tree
Frederick A. Matsen, Aaron Gallagher, Connor McCoy
When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic…