@article{Bluis2003,
  author = {Bluis, John and Shin, Dong Guk},
  doi = {10.1109/BIBE.2003.1188933},
  journal = {Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003},
  pages = {87--94},
  publisher = {IEEE},
  title = {{Nodal distance algorithm: Calculating a phylogenetic tree comparison metric}},
  year = {2003}
}

@incollection{Bocker2013,
  address = {Berlin, Heidelberg},
  author = {B{\"{o}}cker, Sebastian and Canzar, Stefan and Klau, Gunnar W.},
  booktitle = {Algorithms in Bioinformatics. WABI 2013. Lecture Notes in Computer Science, vol 8126},
  doi = {10.1007/978-3-642-40453-5_13},
  editor = {Darling, A. and Stoye, J.},
  pages = {156--169},
  publisher = {Springer},
  title = {{The generalized Robinson-Foulds metric}},
  year = {2013}
}

@article{Bogdanowicz2012,
  author = {Bogdanowicz, Damian and Giaro, Krzysztof},
  doi = {10.1109/TCBB.2011.48},
  issn = {15455963},
  journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  number = {1},
  pages = {150--160},
  title = {{Matching split distance for unrooted binary phylogenetic trees}},
  volume = {9},
  year = {2012}
}

@article{Bogdanowicz2013,
  author = {Bogdanowicz, Damian and Giaro, Krzysztof},
  doi = {10.2478/amcs-2013-0050},
  journal = {International Journal of Applied Mathematics and Computer Science},
  number = {3},
  pages = {669--684},
  title = {{On a matching distance between rooted phylogenetic trees}},
  volume = {23},
  year = {2013}
}

@article{Bogdanowicz2017,
  author = {Bogdanowicz, Damian and Giaro, Krzysztof},
  doi = {10.1089/cmb.2016.0204},
  journal = {Journal of Computational Biology},
  number = {5},
  pages = {422--435},
  title = {{Comparing phylogenetic trees by matching nodes using the transfer distance between partitions}},
  volume = {24},
  year = {2017}
}

@article{Brodal2013,
  author = {Brodal, Gerth St{\o}lting and Fagerberg, Rolf and Mailund, Thomas and Pedersen, Christian N. S. and Sand, Andreas},
  doi = {10.1137/1.9781611973105.130},
  isbn = {9781611972511},
  journal = {SODA '13 Proceedings of the Twenty-Fourth Annual ACM-SIAM Symposium on Discrete Algorithms},
  pages = {1814--1832},
  title = {{Efficient algorithms for computing the triplet and quartet distance between trees of arbitrary degree}},
  year = {2013}
}

@article{Day1986,
  author = {Day, William H.E.},
  doi = {10.1093/sysbio/35.3.325},
  journal = {Systematic Biology},
  number = {3},
  pages = {325--333},
  title = {{Analysis of quartet dissimilarity measures between undirected phylogenetic trees}},
  volume = {35},
  year = {1986}
}

@article{Estabrook1985,
  author = {Estabrook, George F. and McMorris, F. R. and Meacham, Christopher A.},
  doi = {10.2307/2413326},
  journal = {Systematic Zoology},
  number = {2},
  pages = {193--200},
  title = {{Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units}},
  volume = {34},
  year = {1985}
}

@inproceedings{Holt2014,
  address = {Philadelphia, USA},
  author = {Holt, Morten Kragelund and Johansen, Jens and Brodal, Gerth St{\o}lting},
  booktitle = {Proceedings of 16th Workshop on Algorithm Engineering and Experiments (ALENEX) Portland, Oregon, USA},
  publisher = {Society for Industrial and Applied Mathematics (SIAM)},
  title = {{On the scalability of computing triplet and quartet distances}},
  year = {2014}
}

@article{Kullback1951,
  author = {Kullback, S. and Leibler, R. A.},
  doi = {10.1214/aoms/1177729694},
  journal = {The Annals of Mathematical Statistics},
  number = {1},
  pages = {79--86},
  title = {{On information and sufficiency}},
  volume = {22},
  year = {1951}
}

@article{Marczewski1958,
  author = {Marczewski, Edward and Steinhaus, Hugo},
  journal = {Colloquium Mathematicae},
  number = {1},
  pages = {319--327},
  title = {{On a certain distance of sets and the corresponding distance of functions}},
  url = {https://eudml.org/doc/210378},
  volume = {6},
  year = {1958}
}

@article{Nye2006,
  author = {Nye, Tom M W and Li{\`{o}}, Pietro and Gilks, Walter R.},
  doi = {10.1093/bioinformatics/bti720},
  journal = {Bioinformatics},
  number = {1},
  pages = {117--119},
  title = {{A novel algorithm and web-based tool for comparing two alternative phylogenetic trees}},
  volume = {22},
  year = {2006}
}

@article{Penny1985,
  author = {Penny, David and Hendy, M. D.},
  doi = {10.2307/2413347},
  journal = {Systematic Zoology},
  number = {1},
  pages = {75--82},
  title = {{The use of tree comparison metrics}},
  volume = {34},
  year = {1985}
}

@article{Robinson1981,
  author = {Robinson, David F. and Foulds, Leslie R.},
  doi = {10.1016/0025-5564(81)90043-2},
  journal = {Mathematical Biosciences},
  number = {1-2},
  pages = {131--147},
  title = {{Comparison of phylogenetic trees}},
  volume = {53},
  year = {1981}
}

@article{Sand2014,
  author = {Sand, Andreas and Holt, Morten K. and Johansen, Jens and Brodal, Gerth St{\o}lting and Mailund, Thomas and Pedersen, Christian N. S.},
  doi = {10.1093/bioinformatics/btu157},
  issn = {1460-2059},
  journal = {Bioinformatics},
  number = {14},
  pages = {2079--2080},
  title = {{tqDist: a library for computing the quartet and triplet distances between binary or general trees}},
  volume = {30},
  year = {2014}
}

@article{Smith2019,
  author = {Smith, Martin R.},
  doi = {10.1098/rsbl.2018.0632},
  journal = {Biology Letters},
  title = {Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets},
  volume = {15},
  issue = {2},
  pages = {20180632},
  year = {2019}
}

@article{Smith2020,
  author = {Smith, Martin R.},
  title = {Information theoretic {Generalized Robinson-Foulds} metrics for comparing phylogenetic trees},
  journal = {Bioinformatics},
  volume = {36},
  number = {20},
  pages = {5007–5013},
  doi = {10.1093/bioinformatics/btaa614},
  year = {2020}
}

@article{Smith2022,
  author = {Smith, Martin R.},
  title = {Robust analysis of phylogenetic tree space},
  journal = {Systematic Biology},
  doi = {10.1093/sysbio/syab100},
  volume = {71},
  number = {5},
  pages = {1255--1270},
  year = {2022}
}

@article{Steel1993,
  author = {Steel, M. A. and Penny, David},
  doi = {10.1093/sysbio/42.2.126},
  journal = {Systematic Biology},
  number = {2},
  pages = {126--141},
  title = {Distributions of tree comparison metrics---some new results},
  url = {http://www.math.canterbury.ac.nz/~m.steel/Non_UC/files/research/distributions.pdf},
  volume = {42},
  year = {1993}
}

@misc{Ternary,
  title = {Ternary: An {{R}} Package for Creating Ternary Plots},
  author = {Smith, Martin R.},
  year = {2017},
  publisher = {The Comprehensive R Archive Network},
  doi = {10.5281/zenodo.1068997}
}

@misc{TreeSearch,
  author = {Smith, Martin R.},
  doi = {10.5281/zenodo.1042590},
  publisher = {The Comprehensive R Archive Network},
  title = {{TreeSearch: Phylogenetic Tree Search Using Custom Optimality Criteria}},
  year = {2018}
}
