5 papers
Matrix representations and distance metrics for unlabeled ranked phylogenetic networks
Jiayang Wang, Julia A. Palacios, Claudia SolÃs-Lemus
Phylogenetic networks are graphs inferred from molecular sequence data that represent ancestral histories shaped by reticulate processes such as recombination, hybridization, and h…
Generalizing matrix representations to fully heterochronous ranked tree shapes
Chris Jennings-Shaffer, Ziyue, Chen +2
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible wit…
Coalescent Inference for Epidemics with Latent Periods
Isaac H. Goldstein, Julia A. Palacios
Coalescent models are used to study the transmission dynamics of rapidly evolving pathogens from molecular sequence data obtained from infected individuals. However coalescent para…
The space of multifurcating ranked tree shapes: enumeration, lattice structure, and Markov chains
Julie Zhang, Noah A. Rosenberg, Julia A. Palacios
Coalescent models of bifurcating genealogies are used to infer evolutionary parameters from molecular data. However, there are many situations where bifurcating genealogies do not…
Multiple merger coalescent inference of effective population size
Julie Zhang, Julia A. Palacios
Variation in a sample of molecular sequence data informs about the past evolutionary history of the sample's population. Traditionally, Bayesian modeling coupled with the standard…