A modern framework for generalized phylogenetic models of evolution

“Phylogenetics” studies the evolutionary history of relationships between entities.

The entities being studied can be genes, cells, individual organisms, species, but also, less commonly, languages, interaction networks, biological processes - anything that changes over time and undergoes some kind of bifurcation.

With the right data, and with suitable models, we can infer phylogenetic trees as well as the details about the evolutionary processes under which the entities evolve.The purpose of this project is to build an exceptionally general computational and statistical framework for phylogenetic modeling, and to develop a range of new applications that exploit this framework.

The framework itself, which we call MolecularEvolution.jl, is being developed in the Julia language, which is a modern programming language designed specifically for scientific and numerical computing, and the central innovation-by-abstraction that enables the framework exploits Julia’s “multiple dispatch” paradigm.The models that we will develop using this framework include i) new codon models, aiming to improve our ability to detect the molecular footprint of natural selection acting on protein coding genes, ii) new approaches for scalable phylodynamics and phylogeography, which will be especially useful for analyzing large virus genome datasets, iii) cell type “differentiation trees”, where we aim to use phylogenetic approaches to infer differentiation trajectories from single-cell RNAseq data.