TY - JOUR AU - Maiden, M. C. AU - Bygraves, J. A. AU - Feil, E. J. AU - Morelli, G. AU - Russell, J. E. AU - Urwin, R. AU - Zhang, Q. AU - Zhou, J. AU - Zurth, K. AU - Caugant, D. A. AU - Feavers, I. M. AU - Achtman, M. AU - Spratt, B. G. PY - 1998 DA - 1998// TI - Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms JO - Proc Natl Acad Sci USA VL - 95 UR - https://doi.org/10.1073/pnas.95.6.3140 DO - 10.1073/pnas.95.6.3140 ID - Maiden1998 ER - TY - BOOK AU - Huson, D. H. AU - Rupp, R. AU - Scornavacca, C. PY - 2010 DA - 2010// TI - Phylogenetic networks: concepts, algorithms and applications PB - Cambridge University Press CY - New York UR - https://doi.org/10.1017/CBO9780511974076 DO - 10.1017/CBO9780511974076 ID - Huson2010 ER - TY - BOOK AU - Robinson, D. A. AU - Feil, E. J. PY - 2010 DA - 2010// TI - Bacterial population genetics in infectious disease PB - Wiley CY - Hoboken UR - https://doi.org/10.1002/9780470600122 DO - 10.1002/9780470600122 ID - Robinson2010 ER - TY - BOOK AU - Saitou, N. PY - 2013 DA - 2013// TI - Introduction to evolutionary genomics PB - Springer CY - London UR - https://doi.org/10.1007/978-1-4471-5304-7 DO - 10.1007/978-1-4471-5304-7 ID - Saitou2013 ER - TY - JOUR AU - Desper, R. AU - Gascuel, O. PY - 2002 DA - 2002// TI - Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle JO - J Comput Biol VL - 9 UR - https://doi.org/10.1089/106652702761034136 DO - 10.1089/106652702761034136 ID - Desper2002 ER - TY - CHAP AU - Pardi, F. AU - Gascuel, O. ED - Kliman, R. PY - 2016 DA - 2016// TI - Distance-based methods in phylogenetics BT - Encyclopedia of evolutionary biology PB - Elsevier CY - Oxford ID - Pardi2016 ER - TY - JOUR AU - Feil, E. J. AU - Holmes, E. C. AU - Bessen, D. E. AU - Chan, M. -. S. AU - Day, N. P. AU - Enright, M. C. AU - Goldstein, R. AU - Hood, D. W. AU - Kalia, A. AU - Moore, C. E. PY - 2001 DA - 2001// TI - Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences JO - Proc Natl Acad Sci VL - 98 UR - https://doi.org/10.1073/pnas.98.1.182 DO - 10.1073/pnas.98.1.182 ID - Feil2001 ER - TY - JOUR AU - Yang, Z. AU - Rannala, B. PY - 2012 DA - 2012// TI - Molecular phylogenetics: principles and practice JO - Nat Rev Genet VL - 13 UR - https://doi.org/10.1038/nrg3186 DO - 10.1038/nrg3186 ID - Yang2012 ER - TY - JOUR AU - Feil, E. J. AU - Li, B. C. AU - Aanensen, D. M. AU - Hanage, W. P. AU - Spratt, B. G. PY - 2004 DA - 2004// TI - eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data JO - J Bacteriol VL - 186 UR - https://doi.org/10.1128/JB.186.5.1518-1530.2004 DO - 10.1128/JB.186.5.1518-1530.2004 ID - Feil2004 ER - TY - JOUR AU - Francisco, A. P. AU - Bugalho, M. AU - Ramirez, M. PY - 2009 DA - 2009// TI - Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach JO - BMC Bioinform VL - 10 UR - https://doi.org/10.1186/1471-2105-10-152 DO - 10.1186/1471-2105-10-152 ID - Francisco2009 ER - TY - JOUR AU - Saitou, N. AU - Nei, M. PY - 1987 DA - 1987// TI - The neighbor-joining method: a new method for reconstructing phylogenetic trees JO - Mol Biol Evol VL - 4 ID - Saitou1987 ER - TY - JOUR AU - Sokal, R. R. PY - 1958 DA - 1958// TI - A statistical method for evaluating systematic relationships JO - Univ Kans Sci Bull VL - 38 ID - Sokal1958 ER - TY - STD TI - Sergean M, Zhou Z, Alikhan NF, Achtman M. EnteroBase. https://enterobase.warwick.ac.uk/. Accessed 31 Oct 2017. UR - https://enterobase.warwick.ac.uk/ ID - ref13 ER - TY - JOUR AU - Jolley, K. A. AU - Maiden, M. C. J. PY - 2010 DA - 2010// TI - BIGSdb: scalable analysis of bacterial genome variation at the population level JO - BMC Bioinform VL - 11 UR - https://doi.org/10.1186/1471-2105-11-595 DO - 10.1186/1471-2105-11-595 ID - Jolley2010 ER - TY - STD TI - Crochemore M, Francisco AP, Pissis SP, Vaz C. Towards distance-based phylogenetic inference in average-case linear-time. In: Schwartz R, Reinert K (eds.) 17th international workshop on algorithms in bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), vol. 88, p. 9–1914. Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, Dagstuhl, Germany. 2017. https://doi.org/10.4230/LIPIcs.WABI.2017.9. http://drops.dagstuhl.de/opus/volltexte/2017/7652. UR - http://drops.dagstuhl.de/opus/volltexte/2017/7652 ID - ref15 ER - TY - JOUR AU - Manber, U. AU - Myers, G. PY - 1993 DA - 1993// TI - Suffix arrays: a new method for on-line string searches JO - SIAM J Comput VL - 22 UR - https://doi.org/10.1137/0222058 DO - 10.1137/0222058 ID - Manber1993 ER - TY - STD TI - Bender MA, Farach-Colton M. The LCA problem revisited. In: LATIN 2000: theoretical informatics: 4th Latin American symposium. Lecture notes in computer Sscience, vol. 1776, p. 88–94. Springer, Berlin, Heidelberg. 2000. https://doi.org/10.1007/10719839_9. ID - ref17 ER - TY - JOUR AU - Bender, M. A. AU - Farach-Colton, M. AU - Pemmasani, G. AU - Skiena, S. AU - Sumazin, P. PY - 2005 DA - 2005// TI - Lowest common ancestors in trees and directed acyclic graphs JO - J Algorithms VL - 57 UR - https://doi.org/10.1016/j.jalgor.2005.08.001 DO - 10.1016/j.jalgor.2005.08.001 ID - Bender2005 ER - TY - JOUR AU - Kärkkäinen, J. AU - Sanders, P. AU - Burkhardt, S. PY - 2006 DA - 2006// TI - Linear work suffix array construction JO - J ACM VL - 53 UR - https://doi.org/10.1145/1217856.1217858 DO - 10.1145/1217856.1217858 ID - Kärkkäinen2006 ER - TY - STD TI - Ko P, Aluru S. Space efficient linear time construction of suffix arrays. In: Annual symposium on combinatorial pattern matching. Lecture notes in computer science, vol. 2676, p. 200–10. Springer, Berlin, Heidelberg. 2003. https://doi.org/10.1016/j.jda.2004.08.002. ID - ref20 ER - TY - STD TI - Kasai T, Lee G, Arimura H, Arikawa S, Park K. Linear-time longest-common-prefix computation in suffix arrays and its applications. In: Annual symposium on combinatorial pattern matching. Springer. 2001. p. 181–92. https://doi.org/10.1007/3-540-48194-X. ID - ref21 ER - TY - BOOK AU - Papadimitriou, C. H. AU - Steiglitz, K. PY - 1982 DA - 1982// TI - Combinatorial optimization: algorithms and complexity PB - Prentice-Hall Inc CY - Upper Saddle River ID - Papadimitriou1982 ER - TY - JOUR AU - Kruskal, J. B. PY - 1956 DA - 1956// TI - On the shortest spanning subtree of a graph and the traveling salesman problem JO - Proc Am Math Soc VL - 7 UR - https://doi.org/10.1090/S0002-9939-1956-0078686-7 DO - 10.1090/S0002-9939-1956-0078686-7 ID - Kruskal1956 ER - TY - STD TI - B-UMMI: INNUENDO platform. https://github.com/B-UMMI/INNUENDO. Accessed 31 Oct 2017. UR - https://github.com/B-UMMI/INNUENDO ID - ref24 ER - TY - STD TI - INNUENDO: a novel cross-sectorial platform for the integration of genomics in surveillance of foodborne pathogens. http://www.innuendoweb.org/. Accessed 31 Oct 2017. UR - http://www.innuendoweb.org/ ID - ref25 ER - TY - JOUR AU - Ribeiro-Gonçalves, B. AU - Francisco, A. P. AU - Vaz, C. AU - Ramirez, M. AU - Carriço, J. A. PY - 2016 DA - 2016// TI - PHYLOViZ online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkw359 DO - 10.1093/nar/gkw359 ID - Ribeiro-Gonçalves2016 ER - TY - STD TI - B-UMMI: fast MLST searching and querying. https://github.com/B-UMMI/fast-mlst. Accessed 31 Oct 2017. UR - https://github.com/B-UMMI/fast-mlst ID - ref27 ER - TY - STD TI - Mori Y. A lightweight suffix-sorting library. https://github.com/y-256/libdivsufsort. Accessed 31 Oct 2017. UR - https://github.com/y-256/libdivsufsort ID - ref28 ER - TY - STD TI - Larsson NJ, Sadakane K. Suffix sorting implementation to accompany the paper Faster Suffix Sorting. http://www.larsson.dogma.net/qsufsort.c. Accessed 31 Oct 2017. UR - http://www.larsson.dogma.net/qsufsort.c ID - ref29 ER - TY - JOUR AU - Larsson, N. J. AU - Sadakane, K. PY - 2007 DA - 2007// TI - Faster suffix sorting JO - Theor Comput Sci VL - 387 UR - https://doi.org/10.1016/j.tcs.2007.07.017 DO - 10.1016/j.tcs.2007.07.017 ID - Larsson2007 ER - TY - JOUR AU - Francisco, A. P. AU - Vaz, C. AU - Monteiro, P. T. AU - Melo-Cristino, J. AU - Ramirez, M. AU - Carriço, J. A. PY - 2012 DA - 2012// TI - PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods JO - BMC Bioinform VL - 13 UR - https://doi.org/10.1186/1471-2105-13-87 DO - 10.1186/1471-2105-13-87 ID - Francisco2012 ER - TY - JOUR AU - Fredriksson, K. PY - 2004 DA - 2004// TI - Average-optimal single and multiple approximate string matching JO - ACM J Exp Algorithm VL - 9 ID - Fredriksson2004 ER - TY - JOUR AU - Barton, C. AU - Iliopoulos, C. S. AU - Pissis, S. P. PY - 2014 DA - 2014// TI - Fast algorithms for approximate circular string matching JO - Algorithms Mol Biol VL - 9 UR - https://doi.org/10.1186/1748-7188-9-9 DO - 10.1186/1748-7188-9-9 ID - Barton2014 ER - TY - STD TI - Munro JI, Nekrich Y, Vitter JS. Dynamic data structures for document collections and graphs. In: Proceedings of the 34th ACM symposium on principles of database systems. ACM, New York, NY, USA. 2015. https://doi.org/10.1145/2745754.2745778. ID - ref34 ER - TY - JOUR AU - Nascimento, M. AU - Sousa, A. AU - Ramirez, M. AU - Francisco, A. P. AU - Carriço, J. A. AU - Vaz, C. PY - 2017 DA - 2017// TI - PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods JO - Bioinformatics VL - 33 UR - https://doi.org/10.1093/bioinformatics/btw582 DO - 10.1093/bioinformatics/btw582 ID - Nascimento2017 ER - TY - JOUR AU - Page, A. J. AU - Taylor, B. AU - Delaney, A. J. AU - Soares, J. AU - Seemann, T. AU - Keane, J. A. AU - Harris, S. R. PY - 2016 DA - 2016// TI - SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments JO - Microbial Genom VL - 2 ID - Page2016 ER - TY - JOUR AU - Croucher, N. J. AU - Finkelstein, J. A. AU - Pelton, S. I. AU - Mitchell, P. K. AU - Lee, G. M. AU - Parkhill, J. AU - Bentley, S. D. AU - Hanage, W. P. AU - Lipsitch, M. PY - 2013 DA - 2013// TI - Population genomics of post-vaccine changes in pneumococcal epidemiology JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2625 DO - 10.1038/ng.2625 ID - Croucher2013 ER - TY - JOUR AU - Chewapreecha, C. AU - Harris, S. R. AU - Croucher, N. J. AU - Turner, C. AU - Marttinen, P. AU - Cheng, L. AU - Pessia, A. AU - Aanensen, D. M. AU - Mather, A. E. AU - Page, A. J. AU - Salter, S. J. AU - Harris, D. AU - Nosten, F. AU - Goldblatt, D. AU - Corander, J. AU - Parkhill, J. AU - Turner, P. AU - Bentley, S. D. PY - 2014 DA - 2014// TI - Dense genomic sampling identifies highways of pneumococcal recombination JO - Nat Genet VL - 46 UR - https://doi.org/10.1038/ng.2895 DO - 10.1038/ng.2895 ID - Chewapreecha2014 ER - TY - STD TI - National Center for Biotechnology Information: GeneBank. ftp://ftp.ncbi.nih.gov/genomes/archive/old_genbank/Bacteria/. Accessed 31 Oct 2017. UR - ftp://ftp.ncbi.nih.gov/genomes/archive/old_genbank/Bacteria/ ID - ref39 ER -