IcyTree: rapid browser-based visualization for phylogenetic trees and networks von Vaughan, Timothy G

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TreeKnit: Inferring ancestral reassortment graphs of influenza viruses von Barrat-Charlaix, Pierre, Vaughan, Timothy G, Neher, Richard A

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The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies von Huisman, Jana S, Vaughan, Timothy G, Egli, Adrian, Tschudin-Sutter, Sarah, Stadler, Tanja, Bonhoeffer, Sebastian

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Estimating pathogen spread using structured coalescent and birth–death models: A quantitative comparison von Seidel, Sophie, Stadler, Tanja, Vaughan, Timothy G.

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Infectious disease phylodynamics with occurrence data von Featherstone, Leo A., Di Giallonardo, Francesca, Holmes, Edward C., Vaughan, Timothy G., Duchêne, Sebastián

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ReMASTER: improved phylodynamic simulation for BEAST 2.7 von Vaughan, Timothy G

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Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations von Scire, Jérémie, Barido-Sottani, Joëlle, Kühnert, Denise, Vaughan, Timothy G., Stadler, Tanja

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Comparative Epidemiology of Rabbit Haemorrhagic Disease Virus Strains from Viral Sequence Data von Pacioni, Carlo, Hall, Robyn N, Strive, Tanja, Ramsey, David S L, Gill, Mandev S, Vaughan, Timothy G

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BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis von Bouckaert, Remco, Vaughan, Timothy G, Barido-Sottani, Joëlle, Duchêne, Sebastián, Fourment, Mathieu, Gavryushkina, Alexandra, Heled, Joseph, Jones, Graham, Kühnert, Denise, De Maio, Nicola, Matschiner, Michael, Mendes, Fábio K, Müller, Nicola F, Ogilvie, Huw A, du Plessis, Louis, Popinga, Alex, Rambaut, Andrew, Rasmussen, David, Siveroni, Igor, Suchard, Marc A, Wu, Chieh-Hsi, Xie, Dong, Zhang, Chi, Stadler, Tanja, Drummond, Alexei J

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A Multitype Birth–Death Model for Bayesian Inference of Lineage-Specific Birth and Death Rates von BARIDO-SOTTANI, JOËLLE, VAUGHAN, TIMOTHY G., STADLER, TANJA

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The origin and early spread of SARS-CoV-2 in Europe von Nadeau, Sarah A., Vaughan, Timothy G., Scire, Jérémie, Huisman, Jana S., Stadler, Tanja

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Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data von Kühnert, Denise, Stadler, Tanja, Vaughan, Timothy G., Drummond, Alexei J.

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Efficient Bayesian inference under the structured coalescent von Vaughan, Timothy G, Kühnert, Denise, Popinga, Alex, Welch, David, Drummond, Alexei J

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Decoding the Fundamental Drivers of Phylodynamic Inference von Featherstone, Leo A, Duchene, Sebastian, Vaughan, Timothy G

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Estimates of early outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data von Vaughan, Timothy G, Scire, Jérémie, Nadeau, Sarah A, Stadler, Tanja

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Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses von Müller, Nicola F., Stolz, Ugné, Dudas, Gytis, Stadler, Tanja, Vaughan, Timothy G.

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Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model von Kühnert, Denise, Stadler, Tanja, Vaughan, Timothy G., Drummond, Alexei J.

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Inferring Ancestral Recombination Graphs from Bacterial Genomic Data von Vaughan, Timothy G, Welch, David, Drummond, Alexei J, Biggs, Patrick J, George, Tessy, French, Nigel P

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Joint Inference of Migration and Reassortment Patterns for Viruses with Segmented Genomes von Stolz, Ugnė, Stadler, Tanja, Müller, Nicola F, Vaughan, Timothy G

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Estimating Epidemic Incidence and Prevalence from Genomic Data von Vaughan, Timothy G, Leventhal, Gabriel E, Rasmussen, David A, Drummond, Alexei J, Welch, David, Stadler, Tanja

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