Groupe d’expertise : GIPhy – Groupe d’Inférence Phylogénétique

The Institut Pasteur has voluminous activities of microbial strain characterisation, in the context of epidemiological surveillance, biological resource centres collections management, and research. These activities involve National Reference Centers, WHO-collaborative centers, biological resources centers […]

Project context and summary : The phylogenetic position and status of “giant viruses”, formerly called NucleoCytoplasmic Large DNA viruses (NCLDV) or putative order Megavirales, are controversial. Many preliminary phylogenetic analyses have been published, but […]

Contaminant oligonucleotide sequences such as primers and adapters can occur in both ends oƒ high-throughput sequencing (HTS) reads. AlienTrimmer was developed in order to detect and remove such contaminants. ßased on the decomposition oƒ […]

The quality of multiple sequence alignments plays an important role in the accuracy of phylogenetic inference. It has been shown that removing ambiguously aligned regions, but also other sources of bias such as highly […]

JolyTree is a script that implements an alignment-ƒree distance-based procedure ƒor inferring phylogenetic trees ƒrom genome contig sequences. For each pair of genomes, a dissimilarity measure is ƒirst computed and next transƒormed to obtain […]

RΕQ is a program ƒor quickly estimating a conƒidence value at each branch oƒ a distance-based phylogenetic tree. Branch support assessment is commonly based on bootstrap procedures (e.g. Felsenstein 1985, Makarenkov et al. 2010, […]