Olivier Gascuel

We develop phylodynamics models and methods to study viral epidemics, in particular HIV. This new, trendy domain is in between usual mathematical epidemiology, typically based on compartment models, and phylogenetics. The models used in […]

The phylogenetic bootstrap was proposed by Joseph Felsenstein more than 30 years ago. This method, based on resampling and replications, is used extensively to assess the robustness of phylogenetic inferences. Its usefulness, simplicity and […]

The reconstruction of ancestral scenarios is widely used to study the evolution of characters along a phylogenetic tree, for example to infer ancestral molecular characters and their changes in time, or in phylogeography to […]

Drug resistance mutations (DRM) emerge in HIV-1 viruses through selective pressure during antiviral treatment (ART). Acquired drug resistance rates vary depending on duration of ART and type of prescribed regimen. Drug resistance can then […]

Virus discovery and epidemic tracing from high throughput metagenomic sequencing VIROGENESIS is a research project under the EC H2020 framework (2015-2018), that will develop bioinformatics software applications to fully exploit the potential of high-throughput Next-Generation-Sequencing […]

New Generation Phylogeny.fr: Refactoring Phylogeny.fr for innovative phylogenetic services Phylogeny.fr is one of the main server available today able to run phylogenetic analysis pipelines. In the context of scientific workflows, none of the workflow […]

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Free, simple to use web service dedicated to reconstructing and analyzing phylogenetic relationships between molecular sequences.

PastML is a tool for ancestral character reconstruction on phylogenetic trees. The reconstruction of ancestral scenarios is widely used to study the evolution of characters along a phylogenetic tree, for example to infer ancestral […]

BOOSTER is an alternative method for calculating the branch supports of phylogenetic trees, using the bootstrap. With large trees and moderate phylogenetic signal, BOOSTER tends to be more informative than the standard Felsenstein bootstrap […]