references.bib

% Bibliography for Bioinformatics Genomic Analysis Template

@article{blattner1997complete,
    title={The complete genome sequence of Escherichia coli K-12},
    author={Blattner, Frederick R and Plunkett III, Guy and Bloch, Craig A and Perna, Nicole T and Burland, Valerie and Riley, Monica and Collado-Vides, Julio and Glasner, Jeremy D and Rode, Christopher K and Mayhew, George F and others},
    journal={Science},
    volume={277},
    number={5331},
    pages={1453--1462},
    year={1997},
    publisher={American Association for the Advancement of Science},
    doi={10.1126/science.277.5331.1453}
}

@article{tenaillon2010genome,
    title={The population genetics of commensal Escherichia coli},
    author={Tenaillon, Olivier and Skurnik, David and Picard, Bertrand and Denamur, Erick},
    journal={Nature Reviews Microbiology},
    volume={8},
    number={3},
    pages={207--217},
    year={2010},
    publisher={Nature Publishing Group},
    doi={10.1038/nrmicro2298}
}

@article{touchon2009organised,
    title={Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths},
    author={Touchon, Marie and Hoede, Claire and Tenaillon, Olivier and Barbe, Val{\'e}rie and Baeriswyl, Simon and Bidet, Philippe and Bingen, Edouard and Bonacorsi, St{\'e}phane and Bouchier, Christiane and Bouvet, Olivier and others},
    journal={PLoS genetics},
    volume={5},
    number={1},
    pages={e1000344},
    year={2009},
    publisher={Public Library of Science San Francisco, USA},
    doi={10.1371/journal.pgen.1000344}
}

@article{cock2009biopython,
    title={Biopython: freely available Python tools for computational molecular biology and bioinformatics},
    author={Cock, Peter JA and Antao, Tiago and Chang, Jeffrey T and Chapman, Brad A and Cox, Cymon J and Dalke, Andrew and Friedberg, Iddo and Hamelryck, Thomas and Kauff, Frank and Wilczynski, Bartek and others},
    journal={Bioinformatics},
    volume={25},
    number={11},
    pages={1422--1423},
    year={2009},
    publisher={Oxford University Press},
    doi={10.1093/bioinformatics/btp163}
}

@article{altschul1990basic,
    title={Basic local alignment search tool},
    author={Altschul, Stephen F and Gish, Warren and Miller, Webb and Myers, Eugene W and Lipman, David J},
    journal={Journal of molecular biology},
    volume={215},
    number={3},
    pages={403--410},
    year={1990},
    publisher={Elsevier},
    doi={10.1016/S0022-2836(05)80360-2}
}

@article{edgar2004muscle,
    title={MUSCLE: multiple sequence alignment with high accuracy and high throughput},
    author={Edgar, Robert C},
    journal={Nucleic acids research},
    volume={32},
    number={5},
    pages={1792--1797},
    year={2004},
    publisher={Oxford University Press},
    doi={10.1093/nar/gkh340}
}

@article{saitou1987neighbor,
    title={The neighbor-joining method: a new method for reconstructing phylogenetic trees},
    author={Saitou, Naruya and Nei, Masatoshi},
    journal={Molecular biology and evolution},
    volume={4},
    number={4},
    pages={406--425},
    year={1987},
    publisher={Oxford University Press},
    doi={10.1093/oxfordjournals.molbev.a040454}
}

@software{biopython2023,
    title={BioPython: Python tools for computational biology},
    author={Cock, Peter JA and others},
    year={2023},
    url={https://biopython.org/},
    version={1.81}
}

@article{tatusov2000cog,
    title={The COG database: a tool for genome-scale analysis of protein functions and evolution},
    author={Tatusov, Roman L and Galperin, Michael Y and Natale, Darren A and Koonin, Eugene V},
    journal={Nucleic acids research},
    volume={28},
    number={1},
    pages={33--36},
    year={2000},
    publisher={Oxford University Press},
    doi={10.1093/nar/28.1.33}
}