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@article{anisimova2006,
    author = {Anisimova M and Gascuel O},
    year = {2006},
    title = {Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative},
    journal = {Systematic Biology},
    volume = {55},
    number = {4},
    pages = {860--921},
    doi = {10.1080/10635150600755453},
    url = {https://doi.org/10.1080/10635150600755453}
}

@article{anisimova2011,
    author = {Anisimova M and Gil M and Dufayard J-F and Dessimoz C and Gascuel O},
    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,
    author = {Bremer K},
    year = {1988},
    title = {The limits of amino acid sequence data in angiosperm phylogenetic reconstruction},
    journal = {Evolution},
    volume = {42},
    number = {4},
    pages = {795--803},
    doi = {10.1111/j.1558-5646.1988.tb02497.x},
    url = {https://doi.org/10.1111/j.1558-5646.1988.tb02497.x}
}

@article{bremer1994,
    author = {Bremer K},
    year = {1994},
    title = {Branch support and tree stability},
    journal = {Cladistics},
    volume = {10},
    number = {3},
    pages = {295--304},
    doi = {10.1111/j.1096-0031.1994.tb00179.x},
    url = {https://doi.org/10.1111/j.1096-0031.1994.tb00179.x}
}

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

@article{chapus2005,
    author = {Chapus C and Dufraigne C and Edwards S and Giron A and Fertil B and Deschavanne PJ},
    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,
    author = {Cohen E and Chor B},
    year = {2012},
    title = {Detecting phylogenetic signals in eukaryotic whole genome sequences},
    journal = {Journal of Computational Biology},
    volume = {19},
    number = {8},
    pages = {945--956},
    doi = {10.1089/cmb.2012.0122},
    url = {https://doi.org/10.1089/cmb.2012.0122}
}

@article{desper2002,
    author = {Desper R and Gascuel O},
    year = {2002},
    title = {Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle},
    journal = {Journal of Computational Biology},
    volume = {19},
    number = {5},
    pages = {687--705},
    doi = {10.1089/106652702761034136},
    url = {https://doi.org/10.1089/106652702761034136}
}

@article{felsenstein1985,
    author = {Felsenstein J},
    year = {1985},
    title = {Confidence limits on phylogenies: an approach using the bootstrap},
    journal = {Evolution},
    volume = {39},
    number = {4},
    pages = {783--791},
    doi = {10.1111/j.1558-5646.1985.tb00420.x},
    url = {https://doi.org/10.1111/j.1558-5646.1985.tb00420.x}
}

@article{garcia2018,
    author = {Garcia-Hermoso D and Criscuolo A and Lee SC and Legrand M and Chaouat M and Denis B and Lafaurie M and Rouveau M and Soler C and Schaal JV and Mimoun M and Mebazaa A and Heitman J and Dromer F and Brisse S and Bretagne S and Alanio A},
    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},
    number = {2},
    pages = {e00573-18},
    doi = {10.1128/mBio.00573-18},
    url = {http://mbio.asm.org/content/9/2/e00573-18}
}

@article{gascuel1997,
    author = {Gascuel O},
    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},
    number = {7},
    pages = {685--695},
    doi = {10.1093/oxfordjournals.molbev.a025808},
    url = {https://doi.org/10.1093/oxfordjournals.molbev.a025808}
}

@article{henz2005,
    author = {Henz SR and Huson DH and Auch AF and Nieselt-Struwe K and Schuster SC},
    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,
    author = {Hoang DT and Chernomor O and von Haeseler A and Minh BQ and Vinh LS},
    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,
    author = {Hoang DY and Vinh LS and Flouri T and Stamatakis A and von Haeseler A and Minh BQ},
    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,
    author = {House CH and Pellegrini M and Fitz-Gibbon ST},
    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,
    author = {Krajewski C and Dickerman AW},
    year = {1990},
    title = {Bootstrap analysis of phylogenetic trees derived from DNA hydridization distances},
    journal = {Systematic Zoology},
    volume = {39},
    number = {4},
    pages = {383--390},
    doi = {10.2307/2992358},
    url = {https://doi.org/10.2307/2992358}
}

@article{lemoine2018,
    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},
    year = {2018},
    title = {Renewing Felsenstein's phylogenetic bootstrap in the era of big data},
    journal = {Nature},
    volume = {556},
    number = {7702},
    pages = {452--456},
    doi = {10.1038/s41586-018-0043-0 },
    url = {http://dx.doi.org/10.1038/s41586-018-0043-0}
}

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

@article{minh2013,
    author = {Minh BQ and Nguyen MA and von Haeseler A},
    year = {2013},
    title = {Ultrafast approximation for phylogenetic bootstrap},
    journal = {Molecular Biology and Evolution},
    volume = {30},
    number = {5},
    pages = {1188--1195},
    doi = {10.1093/molbev/mst024},
    url = {https://doi.org/10.1093/molbev/mst024}
}

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

@article{saitou1987,
    author = {Saitou N and Nei M},
    year = {1987},
    title = {The neighbor-joining method: a new method for reconstructing phylogenetic trees},
    journal = {Molecular Biology and Evolution},
    volume = {4},
    number = {4},
    pages = {406--425},
    doi = {10.1093/oxfordjournals.molbev.a040454},
    url = {https://doi.org/10.1093/oxfordjournals.molbev.a040454}
}

@article{spencer2007,
    author = {Spencer M and Bryant D and Susko E},
    year = {2007},
    title = {Conditioned genome reconstruction: how to avoid choosing the conditioning genome},
    journal = {Systematic Biology},
    volume = {56},
    number = {1},
    pages = {25--43},
    doi = {10.1080/10635150601156313},
    url = {https://doi.org/10.1080/10635150601156313}
}

@article{studier1988,
    author = {Studier JA and Kepler KJ},
    year = {1988},
    title = {A note on the neighbour-joining method of Saitou and Nei},
    journal = {Molecular Biology and Evolution},
    volume = {5},
    number = {1},
    pages = {729--731},
    doi = {10.1080/10635150601156313},
    url = {https://doi.org/10.1080/10635150601156313}
}

@article{wang2006,
    author = {Wang LS and Warnow T and Moret BM and Jansen RK and Raubeson LA},
    year = {2006},
    title = {Distance-based genome rearrangement phylogeny},
    journal = {Journal of Molecular Evolution},
    volume = {63},
    number = {4},
    pages = {473--483},
    doi = {10.1007/s00239-005-0216-y},
    url = {https://doi.org/10.1007/s00239-005-0216-y}
}

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