The LCA problem revisited, Theoretical Informatics: 4th Latin American Symposium, pp.88-94, 2000. ,
Lowest common ancestors in trees and directed acyclic graphs, Journal of Algorithms, vol.57, issue.2, pp.75-94, 2005. ,
Dense genomic sampling identifies highways of pneumococcal recombination, Nature Genetics, vol.163, issue.3, pp.305-309, 2014. ,
DOI : 10.1101/gr.092759.109
Population genomics of post-vaccine changes in pneumococcal epidemiology, Nature Genetics, vol.45, issue.6, pp.656-663, 2013. ,
Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences, Proceedings of the National Academy of Sciences, pp.182-187, 2001. ,
eburst: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data, Journal of Bacteriology, vol.186, issue.5, pp.1518-1530, 2004. ,
Global optimal eburst analysis of multilocus typing data using a graphic matroid approach, BMC bioinformatics, vol.10, issue.1, 2009. ,
PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods, BMC bioinformatics, vol.13, issue.1, p.87, 2012. ,
Phylogenetic networks: concepts, algorithms and applications, 2010. ,
Linear work suffix array construction, Journal of the ACM, vol.53, issue.6, pp.918-936, 2006. ,
DOI : 10.1145/1217856.1217858
Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications, Annual Symposium on Combinatorial Pattern Matching, pp.181-192, 2001. ,
DOI : 10.1007/3-540-48194-X_17
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.118.8221
Space Efficient Linear Time Construction of Suffix Arrays, Annual Symposium on Combinatorial Pattern Matching, pp.200-210, 2003. ,
DOI : 10.1007/3-540-44888-8_15
On the shortest spanning subtree of a graph and the traveling salesman problem, Proceedings of the American Mathematical Society, vol.7, issue.1, pp.48-50, 1956. ,
Suffix Arrays: A New Method for On-Line String Searches, SIAM Journal on Computing, vol.22, issue.5, pp.935-948, 1993. ,
DOI : 10.1137/0222058
URL : http://webglimpse.net/pubs/suffix.pdf
PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods, Bioinformatics, vol.33, issue.1, pp.128-129 ,
DOI : 10.1093/bioinformatics/btw582
SNP-sites: rapid efficient extraction of SNPs from multi- FASTA alignments, Microbial Genomics, vol.2, issue.4, p.2016 ,
Distance-based methods in phylogenetics, Encyclopedia of Evolutionary Biology, pp.458-465, 2016. ,
URL : https://hal.archives-ouvertes.fr/lirmm-01386569
Bacterial population genetics in infectious disease, 2010. ,
DOI : 10.1002/9780470600122
Introduction to evolutionary genomics, 2013. ,
DOI : 10.1007/978-1-4471-5304-7
URL : https://link.springer.com/content/pdf/bfm%3A978-1-4471-5304-7%2F1.pdf
The neighbor-joining method: a new method for reconstructing phylogenetic trees, Molecular Biology and Evolution, vol.4, issue.4, pp.406-425, 1987. ,
A statistical method for evaluating systematic relationships, Univ Kans Sci Bull, vol.38, pp.1409-1438, 1958. ,