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ABGD, Automatic Barcode Gap Discovery for primary species delimitation
- N. Puillandre, A. Lambert, S. Brouillet, G. Achaz
- Computer Science, BiologyMolecular ecology
- 1 April 2012
Automatic Barcode Gap Discovery is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.
ASAP: assemble species by automatic partitioning
It is demonstrated that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.
Frequency Spectrum Neutrality Tests: One for All and All for One
- G. Achaz
- Computer ScienceGenetics
- 1 September 2009
The framework presented here paves the way for constructing novel tests optimized for specific violations of the standard model that ultimately will help to unravel scenarios of evolution.
Testing for Neutrality in Samples With Sequencing Errors
- G. Achaz
- 1 July 2008
It is shown that even with a moderate number of sequencing errors, neutrality tests based on the frequency spectrum reject neutrality, which implies that analyses of data sets with such errors will systematically lead to wrong inferences of evolutionary scenarios.
cis-Regulatory and protein evolution in orthologous and duplicate genes.
By comparing the genomes of Caenorhabditis elegans and C. briggsae, it is found that protein and regulatory evolution is weakly coupled in orthologs but not paralogs, suggesting that selective pressure on gene expression and protein evolution is quite similar and persists for a significant amount of time following speciation but not gene duplication.
Repseek, a tool to retrieve approximate repeats from large DNA sequences
This work presents an implementation of a two-steps method (seed detection followed by their extension) that detects approximate repeats in large DNA sequences allowing for weighted substitutions and indels in a coherent statistical framework.
Mass extinction in poorly known taxa
- C. Régnier, G. Achaz, A. Lambert, R. Cowie, P. Bouchet, B. Fontaine
- Environmental ScienceProceedings of the National Academy of Sciences
- 8 June 2015
It is estimated that the authors may already have lost 7% of the species on Earth and that the biodiversity crisis is real, based on extrapolation from a random sample of land snail species via two independent approaches.
Population Structure of the Fish-Pathogenic Bacterium Flavobacterium psychrophilum
- P. Nicolas, S. Mondot, G. Achaz, Catherine Bouchenot, J. Bernardet, E. Duchaud
- BiologyApplied and Environmental Microbiology
- 18 April 2008
The nucleotide polymorphisms at 11 protein-coding loci of the core genome in a set of 50 isolates examined showed the existence of several clonal complexes with worldwide geographic distribution but marked association with particular fish species, which could reflect preferential routes of transmission and/or adaptive niche specialization.
Mutations of DEPDC5 cause autosomal dominant focal epilepsies
These findings provided evidence of frequent (37%) loss-of-function mutations in DEPDC5 associated with a broad spectrum of focal epilepsies and the implication of a DEP domain–containing protein that may be involved in membrane trafficking and/or G protein signaling opens new avenues for research.