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new heuristics and parallel computing","volume":"9","author":"D Darriba","year":"2012","journal-title":"Nat Methods"},{"issue":"2","key":"ref77","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1099\/00221287-43-2-159","article-title":"The aerobic pseudomonads: a taxonomic study","volume":"43","author":"RY Stanier","year":"1966","journal-title":"J Gen Microbiol"},{"issue":"2","key":"ref78","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1093\/molbev\/msj030","article-title":"Application of phylogenetic networks in evolutionary studies","volume":"23","author":"DH Huson","year":"2006","journal-title":"Mol Biol Evol"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"98","DOI":"10.3389\/fgene.2013.00098","article-title":"An overview of STRUCTURE: applications, parameter settings, and supporting software","volume":"4","author":"L Porras-Hurtado","year":"2013","journal-title":"Front Genet"},{"issue":"8","key":"ref80","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1093\/molbev\/mss075","article-title":"Bayesian phylogenetics with BEAUti and the BEAST 1.7","volume":"29","author":"AJ Drummond","year":"2012","journal-title":"Mol Biol Evol"},{"issue":"7","key":"ref81","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets","volume":"33","author":"S Kumar","year":"2016","journal-title":"Mol Biol Evol"},{"issue":"3","key":"ref82","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1093\/molbev\/mss265","article-title":"Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci","volume":"30","author":"MS Gill","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"11","key":"ref83","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1093\/bioinformatics\/btp187","article-title":"DnaSP v5: a software for comprehensive analysis of DNA polymorphism data","volume":"25","author":"P Librado","year":"2009","journal-title":"Bioinformatics"},{"issue":"4","key":"ref84","doi-asserted-by":"crossref","first-page":"2665","DOI":"10.1534\/genetics.105.048975","article-title":"A simple and robust statistical test for detecting the presence of recombination","volume":"172","author":"TC Bruen","year":"2006","journal-title":"Genetics"},{"issue":"2","key":"ref85","doi-asserted-by":"crossref","first-page":"e1004041","DOI":"10.1371\/journal.pcbi.1004041","article-title":"ClonalFrameML: efficient inference of recombination in whole bacterial genomes","volume":"11","author":"X Didelot","year":"2015","journal-title":"PLoS Comput Biol"},{"issue":"22","key":"ref86","doi-asserted-by":"crossref","first-page":"2914","DOI":"10.1093\/bioinformatics\/btq549","article-title":"GLOOME: gain loss mapping engine","volume":"26","author":"O Cohen","year":"2010","journal-title":"Bioinformatics"},{"issue":"1","key":"ref87","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1038\/ng.2848","article-title":"Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures","volume":"46","author":"TD Lieberman","year":"2014","journal-title":"Nat Genet"},{"issue":"10","key":"ref88","doi-asserted-by":"crossref","first-page":"e46688","DOI":"10.1371\/journal.pone.0046688","article-title":"Predicting the functional effect of amino acid substitutions and indels","volume":"7","author":"Y Choi","year":"2012","journal-title":"PLoS One"},{"issue":"1","key":"ref89","first-page":"012026","article-title":"SciNet: Lessons Learned from Building a Power-efficient Top-20 System and Data Centre","volume":"256","author":"L Chris","year":"2010","journal-title":"Journal of Physics: Conference Series"},{"issue":"9","key":"ref90","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"M Krzywinski","year":"2009","journal-title":"Genome Res"},{"issue":"W1","key":"ref91","doi-asserted-by":"crossref","first-page":"W242","DOI":"10.1093\/nar\/gkw290","article-title":"Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees","volume":"44","author":"I Letunic","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"ref92","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1186\/s12864-016-3195-z","article-title":"Visualizing tumor evolution with the fishplot package for R","volume":"17","author":"CA Miller","year":"2016","journal-title":"BMC 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