• Publications
  • Influence
Estimating maximum likelihood phylogenies with PhyML.
TLDR
This chapter focuses on phylogenetic tree estimation under the maximum likelihood (ML) principle, a software that implements recent ML phylogenetic methods and algorithms and illustrates the strengths and pitfalls of this program through the analysis of a real data set.
Phylogenomics and the reconstruction of the tree of life
TLDR
This work has demonstrated the power of the phylogenomics approach, which has the potential to provide answers to several fundamental evolutionary questions, but challenges for the future have also been revealed.
Tunicates and not cephalochordates are the closest living relatives of vertebrates
TLDR
It is shown that phylogenetic analyses of the genome sequencing of the appendicularian Oikopleura dioica provide compelling evidence that tunicates, and not cephalochordates, represent the closest living relatives of vertebrates.
Comparative Genomics
  • F. Delsuc
  • Biology
    Lecture Notes in Computer Science
  • 2010
TLDR
A phylogenetic study by Seán G. Brady (2003) sheds new light on the origin of circular mills formed by an isolated group of army ants by showing that the answer to the apparent paradox of circular milling lies at least in part in the evolutionary history of these ants.
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
TLDR
The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons).
The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?
TLDR
It is shown that, according to 95% credibility intervals, the eukaryotic kingdoms diversified 950-1,259 million years ago (Mya), animals diverged from choanoflagellates 761-957 Mya, and the debated age of the split between protostomes and deuterostomes occurred 642-761 Mya.
MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics
TLDR
MitoFinder, a user‐friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries, and shows that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA.
A communal catalogue reveals Earth’s multiscale microbial diversity
TLDR
A meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project is presented, creating both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
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