@article{Arias2004,
  title = {Profile parsimony ({{PP}}): an analysis under implied weights ({{IW}})},
  author = {Arias, J. Salvador and {Miranda-Esquivel}, Daniel Rafael},
  year = {2004},
  volume = {20},
  pages = {56--63},
  doi = {10.1111/j.1096-0031.2003.00001.x},
  journal = {Cladistics},
  number = {1}
}

@article{Aberer2013,
  title = {Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice},
  author = {Aberer, Andre J. and Krompass, Desmithconsnis and Stamatakis, Alexandros},
  year = {2013},
  volume = {62},
  pages = {162--166},
  doi = {10.1093/sysbio/sys078},
  journal = {Systematic Biology},
  number = {1}
}

@article{Bien2011,
  title = {Hierarchical Clustering with Prototypes via Minimax Linkage},
  author = {Bien, Jacob and Tibshirani, Robert},
  year = {2011},
  journal = {Journal of the American Statistical Association},
  volume = {106},
  number = {495},
  pages = {1075--1084},
  doi = {10.1198/jasa.2011.tm10183}
}

@misc{Brazeau2017,
  title = {{{MorphyLib}}: a library for phylogenetic analysis of categorical trait data with inapplicability},
  author = {Brazeau, Martin D. and Smith, Martin R. and Guillerme, Thomas},
  year = {2017},
  doi = {10.5281/zenodo.815372}
}

@article{Brazeau2019,
  author = {Brazeau, Martin D. and Guillerme, Thomas and Smith, Martin R.},
  doi = {10.1093/sysbio/syy083},
  journal = {Systematic Biology},
  pages = {619--631},
  volume = {68},
  issue = {4},
  title = {{An algorithm for morphological phylogenetic analysis with inapplicable data}},
  year = {2019}
}

@article{Carter1990,
  title = {On the distribution of lengths of evolutionary trees},
  author = {Carter, M. and Hendy, M. and Penny, D. and Sz{\'e}kely, L. A. and Wormald, N. C.},
  year = {1990},
  journal = {SIAM Journal on Discrete Mathematics},
  volume = {3},
  number = {1},
  pages = {38--47},
  doi = {10.1137/0403005}
}

@article{Congreve2016,
  author = {Congreve, Curtis R. and Lamsdell, James C.},
  doi = {10.1111/pala.12236},
  issue = {3},
  journal = {Palaeontology},
  pages = {447--465},
  title = {{Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices}},
  volume = {59},
  year = {2016}
}

@article{Congreve2016dd,
  author = {Congreve, Curtis R. and Lamsdell, James C.},
  doi = {10.5061/dryad.7dq0j},
  journal = {Dryad Digital Repository},
  pages = {doi:10.5061/dryad.7dq0j},
  title = {{Data from: Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices}},
  year = {2016}
}

@article{Cotton2008,
  title = {Quantifying the potential utility of phylogenetic characters},
  author = {Cotton, JA and Wilkinson, M},
  year = {2008},
  journal = {Taxon},
  volume = {57},
  number = {1},
  pages = {131--136}
}

@article{Denton2018ee,
  title = {Measuring Inferential Importance of Taxa Using Taxon Influence Indices},
  author = {Denton, John S.S. and Goolsby, Eric W.},
  year = {2018},
  journal = {Ecology and Evolution},
  volume = {8},
  number = {9},
  pages = {4484--4494},
  doi = {10.1002/ece3.3941}
}

@article{Egan2006,
  title = {Support versus corroboration},
  author = {Egan, Mary G.},
  year = {2006},
  volume = {39},
  pages = {72--85},
  doi = {10.1016/j.jbi.2005.11.007},
  journal = {Journal of Biomedical Informatics},
  number = {1},
  series = {Phylogenetic {{Inferencing}}: {{Beyond Biology}}}
}

@article{Faith2001,
  author = {Faith, Daniel P. and Trueman, John W. H.},
  doi = {10.1080/10635150118627},
  journal = {Systematic Biology},
  number = {3},
  pages = {331--350},
  title = {{Towards an inclusive philosophy for phylogenetic inference}},
  volume = {50},
  year = {2001}
}

@article{Farris1969,
  title = {A successive approximations approach to character weighting},
  author = {Farris, James S.},
  year = {1969},
  volume = {18},
  pages = {374--385},
  doi = {10.2307/2412182},
  journal = {Systematic Biology},
  number = {4}
}

@incollection{Farris1983,
  title = {The logical basis of phylogenetic analysis},
  booktitle = {Advances in {{Cladistics}}, {{Vol}}. 2},
  author = {Farris, James S.},
  editor = {Platnick, N. and Funk, V. A.},
  year = {1983},
  pages = {7--36},
  publisher = {{Columbia University Press}},
  address = {{New York}}
}

@article{Farris1989,
  title = {The Retention Index and the Rescaled Consistency Index},
  author = {Farris, James S.},
  year = {1989},
  journal = {Cladistics},
  volume = {5},
  number = {4},
  pages = {417--419},
  doi = {10.1111/j.1096-0031.1989.tb00573.x}
}

@book{Felsenstein2004,
  address = {Sunderland, Massachusetts},
  author = {Felsenstein, Joseph},
  pages = {664},
  publisher = {Sinauer Associates},
  title = {{Inferring phylogenies}},
  year = {2004}
}

@article{Fitch1971,
  title = {Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology},
  author = {Fitch, Walter M.},
  year = {1971},
  journal = {Systematic Biology},
  volume = {20},
  number = {4},
  pages = {406--416},
  doi = {10.1093/sysbio/20.4.406}
}

@article{Goloboff1993,
  title = {Estimating character weights during tree search},
  author = {Goloboff, Pablo A.},
  year = {1993},
  volume = {9},
  pages = {83--91},
  publisher = {{Blackwell Publishing Ltd}},
  doi = {10.1111/j.1096-0031.1993.tb00209.x},
  journal = {Cladistics},
  number = {1}
}

@article{Goloboff1997,
  author = {Goloboff, Pablo A.},
  journal = {Cladistics},
  number = {3},
  pages = {225--245},
  title = {{Self-weighted optimization: tree searches and character state reconstructions under implied transformation costs}},
  doi = {10.1111/j.1096-0031.1997.tb00317.x},
  volume = {13},
  year = {1997}
}

@article{Goloboff1999,
  author = {Goloboff, Pablo A.},
  doi = {10.1006/clad.1999.0122},
  journal = {Cladistics},
  month = {dec},
  number = {4},
  pages = {415--428},
  title = {{Analyzing large data sets in reasonable times: solutions for composite optima}},
  url = {http://doi.wiley.com/10.1006/clad.1999.0122},
  volume = {15},
  year = {1999}
}

@article{Goloboff2008,
  title = {Weighting against homoplasy improves phylogenetic analysis of morphological data sets},
  author = {Goloboff, Pablo A. and Carpenter, James M. and Arias, J. Salvador and Esquivel, Daniel Rafael Miranda},
  year = {2008},
  journal = {Cladistics},
  volume = {24},
  number = {5},
  pages = {758--773},
  doi = {10.1111/j.1096-0031.2008.00209.x}
}

@article{Goloboff2014,
  title = {Extended implied weighting},
  author = {Goloboff, Pablo A.},
  year = {2014},
  volume = {30},
  pages = {260--272},
  doi = {10.1111/cla.12047},
  journal = {Cladistics},
  number = {3}
}

@article{Goloboff2016,
  author = {Goloboff, Pablo A and Catalano, Santiago A},
  doi = {10.1111/cla.12160},
  journal = {Cladistics},
  number = {3},
  pages = {221--238},
  title = {{TNT version 1.5, including a full implementation of phylogenetic morphometrics}},
  volume = {32},
  year = {2016}
}

@article{Goloboff2018,
  title = {Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology},
  author = {Goloboff, Pablo A. and Torres, Ambrosio and Arias, J. Salvador},
  year = {2018},
  volume = {34},
  pages = {407--437},
  doi = {10.1111/cla.12205},
  journal = {Cladistics},
  number = {4}
}

@article{Goloboff2019,
  title = {Likelihood approximations of implied weights parsimony can be selected over the {{Mk}} model by the {{Akaike}} information criterion},
  author = {Goloboff, Pablo A. and Arias, J. Salvador},
  year = {2019},
  journal = {Cladistics},
  volume = {35},
  number = {6},
  pages = {695--716},
  doi = {10.1111/cla.12380}
}

@article{Hartigan1979,
  title = {Algorithm {{AS}} 136: A {{{\emph{K}}}}-Means Clustering Algorithm},
  shorttitle = {Algorithm {{AS}} 136},
  author = {Hartigan, J. A. and Wong, M. A.},
  year = {1979},
  journal = {Journal of the Royal Statistical Society. Series C (Applied Statistics)},
  volume = {28},
  number = {1},
  pages = {100--108},
  doi = {10.2307/2346830}
}

@article{Hopkins2021,
  title = {Incorporating hierarchical characters into phylogenetic analysis},
  year = {2021},
  author = {Hopkins, Melanie J. and St. John, Katherine},
  pages = {syab005},
  doi = {10.1093/sysbio/syab005},
  journal = {Systematic Biology}
}

@article{Kluge1969,
  title = {Quantitative Phyletics and the Evolution of Anurans},
  author = {Kluge, Arnold G. and Farris, James S.},
  year = {1969},
  journal = {Systematic Zoology},
  volume = {18},
  number = {1},
  pages = {1--32},
  doi = {10.1093/sysbio/18.1.1}
}

@article{Kumar2012,
  title = {Statistics and truth in phylogenomics},
  author = {Kumar, Sudhir and Filipski, Alan J. and Battistuzzi, Fabia U. and Kosakovsky Pond, Sergei L. and Tamura, Koichiro},
  year = {2012},
  volume = {29},
  pages = {457--472},
  doi = {10.1093/molbev/msr202},
  journal = {Molecular Biology and Evolution},
  number = {2}
}

@article{Maddison1991,
  title = {Null models for the number of evolutionary steps in a character on a phylogenetic tree},
  author = {Maddison, Wayne P. and Slatkin, M},
  year = {1991},
  volume = {45},
  pages = {1184--1197},
  journal = {Evolution},
  number = {5}
}

@article{Maddison1993,
  title = {Missing data versus missing characters in phylogenetic analysis},
  author = {Maddison, Wayne P.},
  year = {1993},
  volume = {42},
  pages = {576--581},
  doi = {10.1093/sysbio/42.4.576},
  journal = {Systematic Biology},
  number = {4}
}

@article{Maechler2019,
  title = {Cluster: {{Cluster Analysis Basics}} and {{Extensions}}},
  author = {Maechler, Martin and Rousseeuw, Peter and Struyf, Anja and Hubert, Mia and Hornik, Kurt},
  year = {2019},
  journal = {Comprehensive R Archive Network},
  volume = {2.1.0}
}

@article{Mariadassou2012sb,
  title = {Taxon Influence Index: Assessing Taxon-Induced Incongruities in Phylogenetic Inference},
  author = {Mariadassou, Mahendra and {Bar-Hen}, Avner and Kishino, Hirohisa},
  year = {2012},
  journal = {Systematic Biology},
  volume = {61},
  number = {2},
  pages = {337--345},
  doi = {10.1093/sysbio/syr129}
}

@article{Minh2020,
  title = {New methods to calculate concordance factors for phylogenomic datasets},
  author = {Minh, Bui Quang and Hahn, Matthew W and Lanfear, Robert},
  year = {2020},
  volume = {37},
  pages = {2727--2733},
  doi = {10.1093/molbev/msaa106},
  journal = {Molecular Biology and Evolution},
  number = {9}
}

@article{Mir2013,
  title = {A new balance index for phylogenetic trees},
  author = {Mir, Arnau and Rossell{\'o}, Francesc and Rotger, Luc{\'i} A.},
  year = {2013},
  volume = {241},
  pages = {125--136},
  doi = {10.1016/j.mbs.2012.10.005},
  journal = {Mathematical Biosciences},
  number = {1}
}

@article{Muller2005,
  title = {The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and {{Bremer}} support},
  todo_author = {M{\"u}ller, Kai F.},
  author = {Muller, Kai F.},
  year = {2005},
  volume = {5},
  pages = {58},
  doi = {10.1186/1471-2148-5-58},
  journal = {BMC Evolutionary Biology},
  number = {1}
}

@article{Nixon1999,
  author = {Nixon, Kevin C.},
  doi = {10.1111/j.1096-0031.1999.tb00277.x},
  issn = {0748-3007},
  journal = {Cladistics},
  month = {dec},
  number = {4},
  pages = {407--414},
  title = {{The Parsimony Ratchet, a new method for rapid parsimony analysis}},
  volume = {15},
  year = {1999}
}

@article{Phillips2004,
  title = {Genome-scale phylogeny and the detection of systematic biases},
  author = {Phillips, Matthew J and Delsuc, Fr{\'e}d{\'e}ric and Penny, David},
  year = {2004},
  volume = {21},
  pages = {1455--8},
  doi = {10.1093/molbev/msh137},
  journal = {Molecular biology and evolution},
  number = {7}
}

@article{Pol2009,
  title = {Unstable taxa in cladistic analysis: identification and the assessment of relevant characters},
  author = {Pol, Diego and Escapa, Ignacio H.},
  year = {2009},
  journal = {Cladistics},
  volume = {25},
  number = {5},
  pages = {515--527},
  doi = {10.1111/j.1096-0031.2009.00258.x}
}

@article{Shannon1948,
  title = {A mathematical theory of communication},
  author = {Shannon, Claude E.},
  year = {1948},
  journal = {Bell System Technical Journal},
  volume = {27},
  pages = {379--423, 623--656}
}

@article{Simmons2011,
  title = {Spurious 99% bootstrap and jackknife support for unsupported clades},
  author = {Simmons, Mark P and Freudenstein, John V},
  year = {2011},
  volume = {61},
  pages = {177--191},
  publisher = {{Elsevier Inc.}},
  doi = {10.1016/j.ympev.2011.06.003},
  journal = {Molecular Phylogenetics and Evolution},
  number = {1}
}

@article{Smith2014,
  author = {Smith, Martin R. and Ortega-Hern{\'{a}}ndez, Javier},
  doi = {10.1038/nature13576},
  issn = {14764687 00280836},
  journal = {Nature},
  number = {7522},
  pages = {363--366},
  title = {{\textit{Hallucigenia}'s onychophoran-like claws and the case for Tactopoda}},
  volume = {514},
  year = {2014}
}

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

@article{Smith2020,
  title = {Information Theoretic {Generalized Robinson-Foulds} Metrics for Comparing Phylogenetic Trees},
  author = {Smith, Martin R.},
  year = {2020},
  journal = {Bioinformatics},
  volume = {36},
  number = {20},
  pages = {5007--5013},
  doi = {10.1093/bioinformatics/btaa614}
}

@article{SmithCons,
  title = {Using information theory to detect rogue taxa and improve consensus trees},
  author = {Smith, Martin R.},
  journal = {Systematic Biology},
  volume = {71},
  number = {5},
  pages = {1088–1094},
  doi = {10.1093/sysbio/syab099},
  year = {2022}
}

@article{SmithSpace,
  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,
  title = {Distributions on bicoloured binary trees arising from the principle of parsimony},
  author = {Steel, M. A.},
  year = {1993},
  volume = {41},
  pages = {245--261},
  doi = {10.1016/0166-218X(90)90058-K},
  journal = {Discrete Applied Mathematics},
  number = {3}
}

@article{Steel1995,
  title = {Five surprising properties of parsimoniously colored trees},
  author = {Steel, M and Charleston, M},
  year = {1995},
  volume = {57},
  pages = {367--375},
  doi = {10.1016/0092-8240(94)00051-D},
  journal = {Bulletin of Mathematical Biology},
  number = {2}
}

@article{Steel1996,
  title = {A central limit theorem for the parsimony length of trees},
  author = {Steel, Mike and Goldstein, Larry and Waterman, Michael S.},
  year = {1996},
  volume = {28},
  pages = {1051--1071},
  publisher = {{Applied Probability Trust}},
  doi = {10.2307/1428164},
  journal = {Advances in Applied Probability},
  number = {4}
}

@article{Stockham2002,
  title = {Statistically Based Postprocessing of Phylogenetic Analysis by Clustering},
  author = {Stockham, C. and Wang, L.-S. and Warnow, T.},
  year = {2002},
  journal = {Bioinformatics},
  volume = {18},
  number = {Suppl 1},
  pages = {S285-S293},
  doi = {10.1093/bioinformatics/18.suppl_1.S285}
}

@article{Sun2018,
  title = {Hyoliths with Pedicles Illuminate the Origin of the Brachiopod Body Plan},
  author = {Sun, Hai-Jing and Smith, Martin Ross and Zeng, Han and Zhao, Fang-Chen and Li, Guo-Xiang and Zhu, Mao-Yan},
  year = {2018},
  journal = {Proceedings of the Royal Society B},
  volume = {285},
  number = {1887},
  pages = {20181780},
  doi = {10.1098/rspb.2018.1780}
}

@article{Vinther2008,
  author = {Vinther, Jakob and {Van Roy}, Peter and Briggs, Derek E. G.},
  doi = {10.1038/nature06474},
  issn = {1476-4687},
  journal = {Nature},
  number = {7175},
  pages = {185--188},
  publisher = {Nature Publishing Group},
  title = {{Machaeridians are Palaeozoic armoured annelids}},
  volume = {451},
  year = {2008}
}

@article{Wagele2009,
  title = {Phylogenetic support values are not necessarily informative: the case of the {{Serialia}} hypothesis (a mollusk phylogeny)},
  author = {Wagele, J W and Letsch, H and {Klussmann-Kolb}, A and Mayer, C and Misof, B and Wagele, H},
  todo_author = {W{\"a}gele, J W and Letsch, H and {Klussmann-Kolb}, A and Mayer, C and Misof, B and W{\"a}gele, H},
  year = {2009},
  volume = {6},
  pages = {12--29},
  doi = {10.1186/1742-9994-6-12},
  journal = {Frontiers in Zoology},
  number = {1}
}

@article{Whidden2015,
  title = {Quantifying {{MCMC}} Exploration of Phylogenetic Tree Space},
  author = {Whidden, Chris and Matsen, Frederick A.},
  year = {2015},
  journal = {Systematic Biology},
  volume = {64},
  number = {3},
  pages = {472--491},
  publisher = {{Oxford Academic}},
  doi = {10.1093/sysbio/syv006}
}

@article{Wilkinson2017,
  title = {Comments on detecting rogue taxa using {{RogueNaRok}}},
  author = {Wilkinson, Mark and Crotti, Marco},
  year = {2017},
  volume = {15},
  pages = {291--295},
  doi = {10.1080/14772000.2016.1252440},
  journal = {Systematics and Biodiversity},
  number = {4}
}
