Pavel Sagulenko

TL;DR: Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform that presents a real-time view into the evolution and spread of a range of viral pathogens of high public health importance.

TL;DR: TreeTime is presented, a Python-based framework for phylodynamic analysis using an approximate Maximum Likelihood approach that can estimate ancestral states, infer evolution models, reroot trees to maximize temporal signals, estimate molecular clock phylogenies and population size histories and scales linearly with dataset size.

TL;DR: Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualisation platform that presents a real-time view into the evolution and spread of a range of viral pathogens of high public health importance.

TL;DR: TreeTime is presented, a Python based framework for phylodynamic analysis using an approximate Maximum Likelihood approach that can estimate ancestral states, infer evolution models, reroot trees to maximize temporal signals, estimate molecular clock phylogenies and population size histories.

TL;DR: An efficient algorithm to estimate more complex models that allow for different preferences at every site is presented and the accuracy at which such models can be estimated from simulated data is explored.