A. F. Auch, S. R. Henz, B. R. Holland, and M. Göker, Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences, BMC Bioinformatics, vol.7, issue.1, p.350, 2006.

W. Bruno, N. Socci, A. Halpern, S. Casjens, L. Di et al., Weighted Neighbor Joining: a likelihood-based approach to distance-based phylogeny reconstruction, Mathematics in Archaeological and Historical Sciences, vol.17, pp.387-395, 1971.

C. X. Chan, G. Bernard, O. Poirion, J. Hogan, and M. Ragan, Inferring phylogenies of evolving sequences without multiple sequence alignment, Scientific Reports, vol.4, issue.1, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01082062

C. Chapus, C. Dufraigne, S. Edwards, A. Giron, B. Fertil et al., Exploration of phylogenetic data using a global sequence analysis method, Journal of Computational Biology, vol.5, issue.1, pp.945-56, 1993.
URL : https://hal.archives-ouvertes.fr/inserm-00091302

R. Collins, L. Boykin, R. Cruickshank, K. Armstrong, S. Colston et al., Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case, Methods in Ecology and Evolution, vol.3, issue.3, pp.457-465, 2012.

A. Criscuolo, V. Berry, E. P. Douzery, and O. Gascuel, SDM: a fast distance-based approach for (super)tree building in phylogenomics, Systematic Biology, vol.55, issue.5, pp.740-755, 2006.
URL : https://hal.archives-ouvertes.fr/lirmm-00136655

A. Criscuolo, morePhyML: Improving the phylogenetic tree space exploration with PhyML 3, Molecular Phylogenetics and Evolution, vol.61, issue.3, pp.944-948, 2011.

M. Dazas, E. Badell, A. Carmi-leroy, A. Criscuolo, and S. Brisse, Taxonomic status of Corynebacterium diphtheriae biovar Belfanti and proposal of Corynebacterium belfantii sp, International Journal of Systematic and Evolutionary Microbiology, vol.68, issue.12, pp.3826-3831, 2018.

?. Debry, R. Deloger, M. Karoui, M. E. Petit, and M. , A genomic distance based on MUM indicates discontinuity between most bacterial species and genera, Molecular Biology and Evolution, vol.9, issue.3, pp.91-99, 1992.

M. Deng, C. Yu, Q. Liang, R. L. He, and S. S. Yau, A novel method of characterizing genetic sequences: genome space with biological distance and applications, PloS one, vol.6, issue.3, p.17293, 2011.

R. Deng, M. Huang, J. Wang, Y. Huang, J. Yang et al., PTreeRec: phylogenetic tree reconstruction based on genome BLAST distance, Computational Biology and Chemistry, vol.30, issue.4, pp.300-302, 2006.

R. Desper and O. Gascuel, Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle, Journal of Computational Biology, vol.9, issue.5, pp.687-705, 2002.
URL : https://hal.archives-ouvertes.fr/lirmm-00268611

R. Desper and O. Gascuel, Theoretical foundation of the Balanced Minimum Evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting, Molecular Biology and Evolution, vol.21, issue.3, pp.3221-3228, 2003.
URL : https://hal.archives-ouvertes.fr/lirmm-00108569

J. ?-felsenstein, Y. Fofanov, Y. Luo, C. Katili, J. Wang et al., Evolutionary trees from DNA sequences: A maximum likelihood approach, Journal of Molecular Evolution, vol.17, issue.6, pp.2421-2428, 1981.

M. R. Galac and B. P. Lazzaro, Comparative genomics of bacteria in the genus Providencia isolated from wild Drosophila melanogaster, BMC Genomics, vol.13, issue.1, p.612, 2012.

Y. Gao and L. Luo, Genome-based phylogeny of dsDNA viruses by a novel alignment-free method, Gene, vol.492, issue.1, pp.309-323, 2011.

?. Garcia-hermoso, D. Criscuolo, A. Lee, S. C. Legrand, M. Chaouat et al., Outbreak of invasive wound Mucormycosis in a burn unit due to multiple strains of Mucor circinelloides f. circinelloides resolved by whole-genome sequencing, ? Gascuel O, Steel M (2006) Neighbor-Joining revealed, vol.9, pp.1997-2000, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01854232

J. Goris, J. Klappenbach, P. Vandamme, T. Coenye, K. Konstantinidis et al., DNA-DNA hybridization values and their relationship to whole-genome sequence similarities, International Journal of Systematic and Evolutionary Microbiology, vol.57, issue.1, pp.81-91, 2007.

A. ?-guénoche and H. Garreta, Can we have confidence in a tree representation, Computational Biology, pp.45-56, 2001.

K. Hatje and M. Kollmar, A phylogenetic analysis of the brassicales clade based on an alignment-free sequence comparison method. Frontiers in plant science 3: 192, 2012.

B. Haubold, P. Pfaffelhuber, M. Domazet-loso, and T. Wiehe, Estimating mutation distances from unaligned genomes, Journal of Computational Biology, vol.16, issue.10, pp.1487-500, 2009.

B. Haubold, F. Klötzl, and P. Pfaffelhuber, andi: Fast and accurate estimation of evolutionary distances between closely related genomes, Bioinformatics, vol.31, issue.8, pp.1169-1175, 2014.

S. R. Henz, D. H. Huson, A. F. Auch, K. Nieselt-struwe, and S. C. Schuster, Whole-genome prokaryotic phylogeny, Bioinformatics, vol.21, issue.10, pp.2329-2335, 2004.

D. Hillis, J. Huelsenbeck, C. Cunningham, B. R. Holland, K. T. Huber et al., Plots: A tool for analyzing phylogenetic distance data, Molecular Biology and Evolution, vol.264, issue.5159, pp.2051-2059, 1994.

S. Horwege, S. Lindner, M. Boden, K. Hatje, M. Kollmar et al., Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches, Nucleic Acids Research, vol.42, pp.7-11, 2014.

G. Huang, H. Zhou, Y. Li, and L. Xu, Alignment-free comparison of genome sequences by a new numerical characterization, Journal of Theoretical Biology, vol.281, issue.1, pp.107-119, 2011.

J. Huelsenbeck, Performance of phylogenetic methods in simulation, Systematic Biology, vol.44, issue.1, pp.17-48, 1995.

L. ?-jin, M. Nei, T. H. Jukes, and C. R. Cantor, Limitations of the evolutionary parsimony method of phylogenetic analysis, Molecular Biology and Evolution, vol.7, issue.1, pp.21-132, 1969.

M. Kimura and T. Ohta, On the stochastic model for estimation of mutational distance between homologous proteins, Journal of Molecular Evolution, vol.2, issue.1, pp.87-90, 1972.

P. Kolekar, M. Kale, and U. Kulkarni-kale, Alignment-free distance measure based on return time distribution for sequence analysis: applications to clustering, molecular phylogeny and subtyping, Molecular Phylogenetics and Evolution, vol.65, issue.2, pp.510-532, 2012.

P. Kremer, J. A. Lees, M. M. Koopmans, B. Ferwerda, A. Arends et al., Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study, Clinical Microbiology and Infection, vol.23, issue.4, pp.2798-2800, 2015.

C. Leimeister, M. Boden, S. Horwege, S. Lindner, and B. Morgenstern, Fast alignment-free sequence comparison using spaced-word frequencies, Bioinformatics, vol.30, issue.14, pp.1991-2000, 2014.

C. Leimeister, S. Sohrabi-jahromi, and B. Morgenstern, Fast and accurate phylogeny reconstruction using filtered spaced-word matches, Bioinformatics, vol.33, issue.7, pp.971-979, 2017.

Z. Liu and X. Sun, Coronavirus phylogeny based on base-base correlation, International Journal of Bioinformatics Research and Applications, vol.4, issue.2, pp.211-231, 2008.

Y. Li, L. He, R. L. He, S. Yau, E. J. Mctavish et al., Twisted trees and inconsistency of tree estimation when gaps are treated as missing data -The impact of model mis-specification in distance corrections, Molecular Phylogenetics and Evolution, vol.7, issue.1, pp.289-295, 2015.

?. Meier-kolthoff, J. Auch, A. Klenk, H. Göker, and M. , Highly parallelized inference of large genome-based phylogenies, Concurrency and Computation: Practice and Experience, vol.26, issue.10, pp.1715-1729, 2013.

D. Morrison, Increasing the efficiency of searches for the Maximum Likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences, Systematic Biology, vol.56, issue.6, pp.988-1010, 2007.

M. Murra, L. Lützen, A. Barut, R. Zbinden, M. Lund et al., Whole-genome sequencing of Aggregatibacter species isolated from human clinical specimens and description of Aggregatibacter kilianii sp. nov, Journal of Clinical Microbiology, vol.56, issue.7, 2018.

M. Nadimpalli, Y. Vuthy, L. Ad, L. Fabre, A. Criscuolo et al., Meat and fish as sources of extended-spectrum ?-lactamaseproducing Escherichia coli, Cambodia. Emerging Infectious Diseases, vol.25, issue.1, 2019.

M. Nei and S. Kumar, Evolutionary change in DNA sequences, Molecular Evolution and Phylogenetics, pp.33-50, 2000.

A. Nicholson, C. Gulvik, A. Whitney, B. Humrighouse, J. Graziano et al., Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp, Antonie van Leeuwenhoek, vol.111, issue.1, pp.55-72, 2017.

?. O'leary, N. Wright, M. Brister, J. R. Ciufo, S. Haddad et al., Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation, Nucleic Acids Research, vol.44, issue.D1, pp.458-465, 2015.

Y. ?-pauplin, A. Perrin, E. Larsonneur, A. Nicholson, D. Edwards et al., Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain, Journal of Molecular Evolution, vol.51, issue.1, pp.145-158, 2000.

A. Rambaut and N. C. Grassly, Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computer applications in the biosciences, CABIOS, vol.13, issue.3, pp.235-243, 1997.

A. Rokas, B. Williams, N. King, and S. Carroll, Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, vol.425, issue.6960, pp.798-804, 2003.

A. Rzhetsky, T. Sitnikova, N. Saitou, M. Nei, N. Saitou et al., Relative efficiencies of the Fitch-Margoliash, Maximum-Parsimony, Maximum-Likelihood, Minimum-Evolution, and Neighbor-Joining methods of phylogenetic tree construction in obtaining the correct tree, Proceedings of the National Academy of Sciences of the United States of America, vol.13, issue.9, pp.2677-2682, 1987.

G. E. Sims, S. Kim, E. Susko, Y. Inagaki, A. Roger et al., On Inconsistency of the Neighbor-Joining, Least Squares, and Minimum Evolution estimation when substitution processes are incorrectly modeled, University of Kansas Science Bulletin, vol.108, issue.6, pp.115-120, 1982.

F. Tajima, M. Nei, K. Tamura, S. Kumar, N. Topaz et al., BMScan: using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species, The Harvest suite for rapid coregenome alignment and visualization of thousands of intraspecific microbial genomes, vol.1, pp.1727-1736, 1984.

, Genome Biology, vol.15, issue.11

I. Ulitsky, D. Burstein, T. Tuller, and B. Chor, The average common substring approach to phylogenomic reconstruction, Journal of Computational Biology, vol.13, issue.2, pp.336-50, 2006.

Y. Wang, K. Hill, S. Singh, and L. Kari, The spectrum of genomic signatures: from dinucleotides to chaos game representation, Gene, vol.346, pp.173-85, 2005.

Z. Xu and B. Hao, CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes, Nucleic Acids Research, vol.37, pp.174-178, 2009.

L. Yang, X. Zhang, T. Wang, and H. Zhu, Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites, Journal of Computational Biology, vol.20, issue.1, pp.105-116, 1993.

H. Yi, L. Jin, K. Yonezuka, J. Shimodaira, M. Tabata et al., Genome-level comparisons provide insight into the phylogeny and metabolic diversity of species within the genus Lactococcus, Co-phylog: an assembly-free phylogenomic approach for closely related organisms, vol.41, pp.90-92, 1965.

Y. Zhang and S. Qiu, Phylogenomic analysis of the genus Ralstonia based on 686 singlecopy genes, Antonie van Leeuwenhoek, vol.109, issue.1, pp.71-82, 2015.

?. Zhao, X. Zielezinski, A. Vinga, S. Almeida, J. Karlowski et al., BinDash, software for fast genome distance estimation on a typical personal laptop, Bioinformatics, vol.18, issue.1, 2017.