79 citations · 164 across the 20 of their papers we have counts for
4 papers · 1 filter
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…
CRP-Tree: A phylogenetic association test for binary traits
Julie Zhang, Gabriel A. Preising, Molly Schumer +1
An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tr…
Enumeration of binary trees compatible with a perfect phylogeny
Julia A. Palacios, Anand Bhaskar, Filippo Disanto +1
Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a geneal…
phylodyn: an R package for phylodynamic simulation and inference
Michael D. Karcher, Julia A. Palacios, Shiwei Lan +1
We introduce phylodyn, an R package for phylodynamic analysis based on gene genealogies. The package main functionality is Bayesian nonparametric estimation of effective population…