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@article{anisimova2006,
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    author = {Anisimova, M. and Gascuel, O.},
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    year = {2006},
    title = {Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative},
    journal = {Systematic Biology},
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    doi = {10.1080/10635150600755453},
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}

@article{anisimova2011,
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    author = {Anisimova, M. and Gil, M. and Dufayard, J.-F. and Dessimoz, C. and Gascuel, O.},
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    year = {2011},
    title = {Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes},
    journal = {Systematic Biology},
    volume = {60},
    number = {5},
    pages = {685--699},
    doi = {10.1093/sysbio/syr041},
    url = {https://doi.org/10.1093/sysbio/syr041}
}

@article{bremer1988,
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    author = {Bremer, K.},
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    year = {1988},
    title = {The limits of amino acid sequence data in angiosperm phylogenetic reconstruction},
    journal = {Evolution},
    volume = {42},
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    doi = {10.1111/j.1558-5646.1988.tb02497.x},
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}

@article{bremer1994,
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    author = {Bremer, K.},
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    year = {1994},
    title = {Branch support and tree stability},
    journal = {Cladistics},
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}

@inproceedings{buneman1971,
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    author = {Buneman, P.},
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    year = {1971},
    title = {The recovery of trees from measures of dissimilarity},
    booktitle= {Mathematics in Archaeological and Historical Sciences},
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    editor = {Hodson, F.~R. and Kendall, D.~G. and Tautu, P.},
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    pages = {387--395},
    publisher = {Edinburgh University Press},
    address = {Edimburgh},
    url = {http://homepages.inf.ed.ac.uk/opb/homepagefiles/phylogeny-scans/manuscripts.pdf}
}

@article{chapus2005,
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    author = {Chapus, C. and Dufraigne, C. and Edwards, S. and Giron, A. and Fertil, B. and Deschavanne, P.~J.},
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    year = {2005},
    title = {Exploration of phylogenetic data using a global sequence analysis method},
    journal = {BMC Evolutionary Biology},
    volume = {5},
    pages = {63},
    doi = {10.1186/1471-2148-5-63},
    url = {https://doi.org/10.1186/1471-2148-5-63}
}

@article{cohen2012,
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    author = {Cohen, E. and Chor, B.},
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    year = {2012},
    title = {Detecting phylogenetic signals in eukaryotic whole genome sequences},
    journal = {Journal of Computational Biology},
    volume = {19},
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    doi = {10.1089/cmb.2012.0122},
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}

@article{desper2002,
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    author = {Desper, R. and Gascuel, O.},
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    year = {2002},
    title = {Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle},
    journal = {Journal of Computational Biology},
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    doi = {10.1089/106652702761034136},
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}

@article{felsenstein1985,
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    author = {Felsenstein, J.},
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    year = {1985},
    title = {Confidence limits on phylogenies: an approach using the bootstrap},
    journal = {Evolution},
    volume = {39},
    number = {4},
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    doi = {10.1111/j.1558-5646.1985.tb00420.x},
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}

@article{garcia2018,
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    author = {Garcia-Hermoso, D. and Criscuolo, A. and Lee, S.~C. and Legrand, M. and Chaouat, M. and Denis, B. and Lafaurie, M. and Rouveau, M. and Soler, C. and Schaal, J.~V. and Mimoun, M. and Mebazaa, A. and Heitman, J. and Dromer, F. and Brisse, S. and Bretagne, S. and Alanio, A.},
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    year = {2018},
    title = {Outbreak of invasive wound mucormycosis in a burn unit due to multiple strains of Mucor circinelloides f. circinelloides resolved by whole-genome sequencing},
    journal = {MBio},
    volume = {9},
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    pages = {e00573-18},
    doi = {10.1128/mBio.00573-18},
    url = {http://mbio.asm.org/content/9/2/e00573-18}
}

@article{gascuel1997,
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    author = {Gascuel, O.},
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    year = {1997},
    title = {BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data},
    journal = {Molecular Biology and Evolution},
    volume = {14},
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    doi = {10.1093/oxfordjournals.molbev.a025808},
    url = {https://doi.org/10.1093/oxfordjournals.molbev.a025808}
}

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@inproceedings{guenoche2001,
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    author = {Guénoche, A. and Garreta, H.},
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    year = {2001},
    title = {Can we have confidence in a tree representation?},
    booktitle= {Computational Biology},
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    editor = {Gascuel, O. and Sagot, M.-F.},
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    pages = {45--56},
    publisher = {Springer Berlin Heidelberg},
    address = {Berlin, Heidelberg},
    doi = {10.1007/3-540-45727-5_5},
    url = {http://iml.univ-mrs.fr/editions/biblio/guenoche/QualiTree-1.pdf}
}

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@article{henz2005,
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    author = {Henz, S.~R. and Huson, D.~H. and Auch, A.~F. and {Nieselt-Struwe}, K. and Schuster, S.~C.},
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    year = {2005},
    title = {Whole-genome prokaryotic phylogeny},
    journal = {Bioinformatics},
    volume = {21},
    number = {10},
    pages = {2329--2335},
    doi = {10.1093/bioinformatics/bth324},
    url = {https://doi.org/10.1093/bioinformatics/bth324}
}

@article{hoang2018a,
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    author = {Hoang, D.~T. and Chernomor, O. and {von Haeseler}, A. and Minh, B.~Q. and Vinh, L.~S.},
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    year = {2018},
    title = {UFBoot2: improving the ultrafast bootstrap approximation},
    journal = {Molecular Biology and Evolution},
    volume = {35},
    number = {2},
    pages = {518--522},
    doi = {10.1093/molbev/msx281},
    url = {https://doi.org/10.1093/molbev/msx281}
}

@article{hoang2018b,
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    author = {Hoang, D.~T. and Vinh, L.~S. and Flouri, T. and Stamatakis, A. and {von Haeseler}, A. and Minh, B.~Q.},
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    year = {2018},
    title = {MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation},
    journal = {BMC Evolutionary Biology},
    volume = {18},
    number = {1},
    pages = {11},
    doi = {10.1186/s12862-018-1131-3},
    url = {https://doi.org/10.1186/s12862-018-1131-3}
}

@article{house2014,
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    author = {House, C.~H. and Pellegrini, M. and {Fitz-Gibbon}, S.~T.},
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    year = {2014},
    title = {Genome-wide gene order distances support clustering the gram-positive bacteria},
    journal = {Frontiers in Microbiology},
    volume = {5},
    pages = {785},
    doi = {10.3389/fmicb.2014.00785},
    url = {https://dx.doi.org/10.3389%2Ffmicb.2014.00785}
}

@article{krajewski1990,
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    author = {Krajewski, C. and Dickerman, A.~W.},
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    year = {1990},
    title = {Bootstrap analysis of phylogenetic trees derived from DNA hydridization distances},
    journal = {Systematic Zoology},
    volume = {39},
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}

@article{lemoine2018,
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    author = {Lemoine, F. and Domelevo-Entfellner, J.-B. and Wilkinson, E. and Correia, D. and {Davila Felipe}, M. and {De Oliveira}, T. and Gascuel, O.},
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    year = {2018},
    title = {Renewing Felsenstein's phylogenetic bootstrap in the era of big data},
    journal = {Nature},
    volume = {556},
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}

@article{makarenkov2010,
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    author = {Makarenkov, V. and Boc, A. and Xie, J. and Peres-Neto, P. and Lapointe, F.-J. and Legendre, P.},
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    year = {2010},
    title = {Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees},
    journal = {BMC Evolutionary Biology},
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    url = {https://doi.org/10.1186/1471-2148-10-250}
}

@article{minh2013,
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    author = {Minh, B.~Q. and Nguyen, M.~A. and {von Haeseler}, A.},
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    year = {2013},
    title = {Ultrafast approximation for phylogenetic bootstrap},
    journal = {Molecular Biology and Evolution},
    volume = {30},
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}

@incollection{pardi2016,
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    author = {Pardi, F. and Gascuel, O.},
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    year = {2016},
    title = {Distance-based methods in phylogenetics},
    booktitle = {Encyclopedia of Evolutionary Biology},
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    editor = {Kliman, R.},
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    publisher = {Academic Press},
    pages = {458--465},
    url = {https://hal-lirmm.ccsd.cnrs.fr/lirmm-01386569}
}

@article{saitou1987,
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    author = {Saitou, N. and Nei, M.},
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    year = {1987},
    title = {The neighbor-joining method: a new method for reconstructing phylogenetic trees},
    journal = {Molecular Biology and Evolution},
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}

@article{spencer2007,
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    author = {Spencer, M. and Bryant, D. and Susko, E.},
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    year = {2007},
    title = {Conditioned genome reconstruction: how to avoid choosing the conditioning genome},
    journal = {Systematic Biology},
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    doi = {10.1080/10635150601156313},
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}

@article{studier1988,
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    author = {Studier, J.~A. and Kepler, K.~J.},
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    year = {1988},
    title = {A note on the neighbour-joining method of Saitou and Nei},
    journal = {Molecular Biology and Evolution},
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}

@article{wang2006,
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    author = {Wang, L.~S. and Warnow, T. and Moret, B.~M. and Jansen, R.~K. and Raubeson, L.~A.},
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    year = {2006},
    title = {Distance-based genome rearrangement phylogeny},
    journal = {Journal of Molecular Evolution},
    volume = {63},
    number = {4},
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    doi = {10.1007/s00239-005-0216-y},
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}

@article{zaretskii1965,
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    author = {Zaretskii, Z.~A.},
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    year = {1965},
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    title = {Constructing a tree on the basis of a set of distances between the hanging vertices [in Russian]},
    note = {ПОСТРОЕНИЕ ДЕРЕВА ПО НАБОРУ РАССТОЯНИЙ МЕЖДУ ВИСЯЧИМИ ВЕРШИНАМИ [real title]},
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    journal = {Uspekhi Matematicheskikh Nauk},
    volume = {20},
    number = {6},
    pages = {94--96},
    url = {http://mi.mathnet.ru/eng/umn6134}
}