Bioinformatique évolutive

We received a grant by Campus France (PHC Carlos J Finlay, 2019-20210) to collaborate with the team of Dr Vivian Kourí Cardellá from Instituto de Medicina Tropical Pedro Kourí (Habana) on the dynamics of […]

Luc Blassel’s PhD project (funded by PRAIRIE – supervision O. Gascuel) is to apply machine learning techniques to the analysis of sequence data. Traditional sequence alignment and analysis methods might not be able to […]

Phylogeography is a field of study concerned with the principles and processes governing the geographic distributions of genealogical lineages, especially those within or among closely related species. [Avise et al. Ann Rev Ecol Syst […]

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 […]

We published in Nature in 2018 a renewed version of the phylogenetic bootstrap, which was proposed by Joseph Felsenstein more than 30 years ago. This method, based on resampling and replications, is used extensively […]

In 2019 we published several results on ancestral reconstruction, notably in Molecular Biology and Evolution, Systematic Biology and Bioinformatics. The reconstruction of ancestral scenarios is widely used to study the evolution of characters along […]

HIV-1 drug resistance mutations (DRMs) can be dangerous not only on the individual level but also for the whole population. Acquired drug resistance (ADR) appears under drug selective pressure and limits the choice of […]

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 […]

The first cases of the COVID-19 pandemic emerged in December 2019. Until the end of February 2020, the number of available genomes was below 1,000, and their multiple alignment was easily achieved using standard […]

Goalign and Gotree are comand line tools aiming at manipulating multiple alignments and phylogenetic trees. They are implemented in Go language. Goalign aims at handling multiple alignments in Phylip, Fasta, Nexus, and Clustal formats, […]

NGPhylogeny.fr is a 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 […]