Remco Bouckaert

Jul 15, 2024 | biorxiv.org | Caroline Colijn |Matthew Hall |Remco Bouckaert |Simon Fraser

AbstractWe introduce and apply Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories (BREATH), a method to simultaneously construct phylogenetic trees and transmission trees using sequence data for a person-to-person outbreak. BREATH's transmission process that accounts for a flexible natural history of infection (including a latent period if desired) and a separate process for sampling.

Jan 30, 2024 | biorxiv.org | Remco Bouckaert

AbstractIn this paper, we study the distance matrix as a representation of a phylogeny by way of hierarchical clustering. By defining a multivariate normal distribution on (a subset of) the entries in a matrix, this allows us to represent a distribution over rooted time trees. Here, we demonstrate tree distributions can be represented accurately this way for a number of published tree distributions.

Oct 23, 2023 | biorxiv.org | Remco Bouckaert

AbstractVariational Bayesian methods work well when the distribution of interest can be represented by a Euclidian space using a bijective transformation between phylogenies and their representation. Until now, full phylogenetic inference has been hampered by the lack of such transformation. Here, we study the distance matrix as a representation of a phylogeny through single link clustering.