Clostridium baratii core-genome
Aligned recombination-purged core-genome estimated from 7 C. baratii isolates in FASTA format
Mazuet C, Legeay C, Sautereau J, Bouchier C, Criscuolo A, Bouvet P, Trehard H, Jourdan Da Silva N, Popoff M (2017)
Characterization of Clostridium baratii Type F strains responsible for an outbreak of botulism linked to beef meat consumption in France.
PLOS Currents Outbreaks, Edition 1.
doi:10.1371/currents.outbreaks.6ed2fe754b58a5c42d0c33d586ffc606
Bordetella pertussis core-gene
Concatenated multiple sequence alignments of 2,038 cgMLST loci from 55 B. pertussis isolates in FASTA format
Bouchez V, Guglielmini J, Dazas M, Landier A, Toubiana J, Guillot S, Criscuolo A, Brisse S (2018)
Genomic sequencing of Bordetella pertussis for epidemiology and global surveillance of whooping cough.
Emerging Infectious Diseases, 24:988–994. doi:10.3201/eid2406.171464
Mucor circinelloides f. circinelloides de novo genome assemblies
25 FASTA-formatted files, each corresponding to assembled scaffold sequences of the genome of a M. circinelloides f. circinelloides isolate
Garcia-Hermoso D, Criscuolo A, Lee SC, Legrand M, Chaouat M, Denis B, Lafaurie M, Rouveau M, Soler C, Schaal JV, Mimoun M, Mebazaa A, Heitman J, Dromer F, Brisse S, Bretagne S, Alanio A (2018)
Outbreak of invasive wound Mucormycosis in a burn unit due to multiple strains of Mucor circinelloides f. circinelloides resolved by whole-genome sequencing.
mBio, 9:e00573–18. doi:10.1128/mBio.00573-18
Clostridium perfringens core-genome
Aligned recombination-purged core-genome estimated from 115 C. perfringens isolates in FASTA format
Diancourt L, Sautereau J, Criscuolo A, Popoff MR (2019)
Two Clostridium perfringens type E isolates in France.
Toxins, 11:E138. doi:10.3390/toxins11030138
Corynebacterium belfantii core-genome
Read mapping-based core-genome estimated from 6 C. belfantii isolates in FASTA format
Pivot D, Fanton A, Badell-Ocando E, Benouachkou M, Astruc K, Huet F, Amoureux L, Neuwirth C, Criscuolo A, Aho S, Toubiana J, Brisse S (2019)
Carriage of a single strain of nontoxigenic Corynebacterium diphtheriae bv. Belfanti (Corynebacterium belfantii) in four patients with cystic fibrosis.
Journal of Clinical Microbiology, 57:00042–19. doi:10.1128/JCM.00042-19
Simulation data for testing alignment-free genome distance estimates
Twelve XZ-compressed files containing 500 pairs of genome sequences (and associated parameters) simulated using SeqGen with the GTR+Γ evolutionary model
Criscuolo A (2019)
A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies.
Research Ideas and Outcomes, 5:e36178. doi:10.3897/rio.5.e36178
Simulated pairs of nucleotide sequences for testing (alignment-free) genome distance estimate methods
120 XZ-compressed files containing 200 pairs of genome sequences (and associated parameters) simulated using INDELible with the GTR+Γ evolutionary model
Criscuolo A (2020)
On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference.
F1000Research, 9:1309. doi:10.12688/f1000research.26930.1
Model trees and associated simulated nucleotide sequences for testing phylogenetic inference methods
142 tar.gz archives containing phylogenomic datasets simulated using INDELible with the GTR+Γ evolutionary model
Criscuolo A (2020)
On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference.
F1000Research, 9:1309. doi:10.12688/f1000research.26930.1