Viruses of Respiratory Infections (including Influenza and SARS-CoV-2)

Respiratory viruses are the cause of major epidemics worldwide. In particular, Influenza viruses, respiratory syncytial viruses (RSV), and more recently SARS-CoV-2, have been leading causes of hospitalizations for acute respiratory infections. The evolution of […]

Routine virological surveillance is crucial for monitoring viral epidemics, particularly for identifying concerning mutations, evaluating viral genomic diversity, and predicting future dominant clades. High-throughput sequencing and efficient bioinformatics methods have been pivotal in this […]

The SEQ4EPI project, led by Santé publique France and the CNR Virus of Respiratory Infections, aims to support the long-term sustainability of genomic surveillance systems developed during the pandemic and prepare them for future […]

In 2022, the European Centre for Disease Prevention and Control (ECDC) granted a new framework contract to a consortium of twelve institutes from eight European countries. The project, titled “AURORAE,” focuses on “Supporting microbiology-related […]

About the Nanopore User Group: The Nanopore User Group at Institut Pasteur was established in 2019 with the primary goal of fostering collaboration, sharing knowledge, and advancing the application of Oxford Nanopore Technologies (ONT) […]

Due to the frequentist nature of bootstrap sampling, the expected support of a branch corresponding to a single mutation is ∼63%, even though it is highly likely to be correct. Here we propose a […]

ConDor detects convergent mutations in large protein alignments. It is available as a standalone workflow and a web service. ConDor implements a two-component approach to detect mutations subject to convergent evolution in protein alignments. […]

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. NGPhylogeny.fr is flexible in terms of tools and workflows, easily installable, and more scalable. It […]

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 […]