arXiv subjects

Chantal Abergel

Publications and source records attributed to Chantal Abergel.

2 recordsLinked to original sources

arXiv2026

Phylogeny.fr: the phylogenetic platform designed for non-specialists

Phylogenetic analysis has become a standard approach across many areas of biology, yet the growing complexity of phylogenetic methods and software remains a major obstacle for non-specialists. Since its launch in 2008, Phylogeny.fr has provided an accessible web platform for building phylogenetic trees using widely accepted methods without requiring local software installation. Here, we present a major redesign and modernization of the service. The new version integrates state-of-the-art tools while preserving historical programs for legacy support and relies on modern web architecture and HPC infrastructure. New interactive React-based viewers, ReSeqt and Reactree, provide intuitive exploration and publication-ready visualization of alignments and trees. The Blast-Explorer companion tool has also been updated and now includes clustering options. By combining ease of use, methodological flexibility, and modern phylogenetic tools, the new Phylogeny.fr addresses the needs of researchers, teachers, and students seeking accessible and reliable phylogenetic analyses.

q-bio.QM↗

arXiv2005

Mimivirus and the emerging concept of "giant" virus

The recently discovered Acanthamoeba polyphaga Mimivirus is the largest known DNA virus. Its particle size (>400 nm), genome length (1.2 million bp) and large gene repertoire (911 protein coding genes) blur the established boundaries between viruses and parasitic cellular organisms. In addition, the analysis of its genome sequence identified new types of genes not expected to be seen in a virus, such as aminoacyl-tRNA synthetases and other central components of the translation machinery. In this article, we examine how the finding of a giant virus for the first time overlapping with the world of cellular organisms in terms of size and genome complexity might durably influence the way we look at microbial biodiversity, and force us to fundamentally revise our classification of life forms. We propose to introduce the word "girus" to recognize the intermediate status of these giant DNA viruses, the genome complexity of which make them closer to small parasitic prokaryotes than to regular viruses.

q-bio.PE↗