otcetera.bib

@article{SmithBH2013,
  title={Analyzing and synthesizing phylogenies using tree alignment graphs},
  author={Stephen A. Smith and Joseph W. Brown and Cody E. Hinchliff},
  journal={PLoS computational biology},
  volume={9},
  number={9},
  pages={e1003223},
  year={2013},
  publisher={Public Library of Science},
  url={http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003223},
  doi={10.1371/journal.pcbi.1003223}
}
@article{JanssonLL2012,
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  journal={SIAM Journal on Computing},
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  year={2012},
  publisher={SIAM}
}

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@article{HolmLT2001,
  title={Poly-logarithmic deterministic fully-dynamic algorithms for connectivity, minimum spanning tree, 2-edge, and biconnectivity},
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  publisher={ACM}
}

@article{Semple2003,
  title={Reconstructing minimal rooted trees},
  author={Semple, Charles},
  journal={Discrete applied mathematics},
  volume={127},
  number={3},
  pages={489--503},
  year={2003},
  publisher={Elsevier}
}

@article{ByrkaGJ2010,
  title={New results on optimizing rooted triplets consistency},
  author={Byrka, Jaroslaw and Guillemot, Sylvain and Jansson, Jesper},
  journal={Discrete Applied Mathematics},
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  pages={1136--1147},
  year={2010},
  publisher={Elsevier}
}

@article{HinchliffEtAl2015,
author = {Hinchliff, Cody E. and Smith, Stephen A. and Allman, James F. and Burleigh, J. Gordon and Chaudhary, Ruchi and Coghill, Lyndon M. and Crandall, Keith A. and Deng, Jiabin and Drew, Bryan T. and Gazis, Romina and Gude, Karl and Hibbett, David S. and Katz, Laura A. and Laughinghouse, H. Dail and McTavish, Emily Jane and Midford, Peter E. and Owen, Christopher L. and Ree, Richard H. and Rees, Jonathan A. and Soltis, Douglas E. and Williams, Tiffani and Cranston, Karen A.}, 
title = {Synthesis of phylogeny and taxonomy into a comprehensive tree of life},
volume = {112}, 
number = {41}, 
pages = {12764-12769}, 
year = {2015}, 
doi = {10.1073/pnas.1423041112}, 
abstract ={Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.}, 
URL = {http://www.pnas.org/content/112/41/12764.abstract}, 
eprint = {http://www.pnas.org/content/112/41/12764.full.pdf}, 
journal = {Proceedings of the National Academy of Sciences} 
}