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paper.bib
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@Article{abella12,
Title = {\textit{{K}retzoiarctos} gen. nov., the Oldest Member of the Giant Panda Clade},
Author = {Juan Abella and David M. Alba and Josep M. Robles and Alberto Valenciano and Cheyenn Rotgers and Ra\"ul Carmona and Plinio Montoya and Jorge Morales},
Journal = {PLoS One},
Year = {2012},
Pages = {e48985},
Volume = {17}
}
@Article{abella2011,
Title = {Una nueva especie de \textit{{A}griarctos} ({A}iluropodinae, {U}rsidae, {C}arnivora) en la localidad de {N}ombrevilla 2 ({Z}aragoza, {E}spa{\~n}a)},
Author = {Abella, J and Montoya, P and Morales, J},
Journal = {Estudios Geol{\'o}gicos},
Year = {2011},
Number = {2},
Pages = {187--191},
Volume = {67}
}
@article {Baum979,
author = {Baum, David A. and Smith, Stacey DeWitt and Donovan, Samuel S. S.},
title = {The Tree-Thinking Challenge},
volume = {310},
number = {5750},
pages = {979--980},
year = {2005},
doi = {10.1126/science.1117727},
publisher = {American Association for the Advancement of Science},
issn = {0036-8075},
URL = {http://science.sciencemag.org/content/310/5750/979},
eprint = {http://science.sciencemag.org/content/310/5750/979.full.pdf},
journal = {Science}
}
@Manual{shiny,
title = {shiny: Web Application Framework for {R}},
author = {Winston Chang and Joe Cheng and JJ Allaire and Yihui Xie and Jonathan McPherson},
year = {2018},
note = {R package version 1.1.0},
url = {https://CRAN.R-project.org/package=shiny},
}
@Book{Darwin1859,
Title = {On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life},
Author = {Darwin, Charles},
Publisher = {Murray, London},
Year = {1859},
Owner = {hoehna},
Timestamp = {2013.10.12}
}
@article{FarrisKluge,
author = {Farris, James S. and Kluge, Arnold G. and Eckardt, Michael J.},
title = {A Numerical Approach to Phylogenetic Systematics},
journal = {Systematic Biology},
volume = {19},
number = {2},
pages = {172-189},
year = {1970},
doi = {10.2307/2412452},
}
@Article{Felsenstein1978,
Title = {The Number of Evolutionary Trees},
Author = {Felsenstein, J.},
Journal = {Systematic Zoology},
Year = {1978},
Number = {1},
DOI = {10.2307/2412810},
Pages = {27--33},
Volume = {27},
Abstract = {A simple method of counting the number of possible evolutionary trees is presented. The trees are assumed to be rooted, with labelled tips but unlabelled root and unlabelled interior nodes. The method allows multifurcations as well as bifurcations. It makes use of a simple recurrence relation for T(n,m), the number of trees with n labelled tips and m unlabelled interior nodes. A table of the total number of trees is presented up to n = 22. There are 282,137,824 different trees having 10 tip species, and over 8.87 x 10<sup>23</sup> different trees having 20 tip species. The method is extended to count trees some of whose interior nodes may be labelled. The principal uses of these numbers will be to double-check algorithms and notation systems, and to frighten taxonomists.},
Copyright = {Copyright ? 1978 Society of Systematic Biologists},
ISSN = {00397989},
Jstor_articletype = {primary_article},
Jstor_formatteddate = {Mar., 1978},
Owner = {hoehna},
Publisher = {Taylor \& Francis, Ltd. for the Society of Systematic Biologists},
Timestamp = {2009.08.05}
}
@Article{Felsenstein1973,
Title = {{Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters}},
Author = {Felsenstein, J.},
Journal = {Systematic Zoology},
Year = {1973},
Number = {3},
Pages = {240--249},
Volume = {22},
DOI = {10.1093/sysbio/22.3.240},
Owner = {shhn001},
Publisher = {JSTOR},
Timestamp = {2008.04.02}
}
@article{feng,
title={Progressive sequence alignment as a prerequisite to correct phylogenetic trees},
author={Feng, D. and Doolittle, R. F.},
journal={Journal of Molecular Evolution},
volume={25},
number={4},
pages={351--360},
doi = {10.1007/BF02603120},
year={1987},
publisher={Springer}
}
@article{gower1969,
title={Minimum spanning trees and single linkage cluster analysis},
author={Gower, John C and Ross, Gavin JS},
journal={Applied Statistics},
pages={54--64},
year={1969},
Doi = {10.2307/2346439},
publisher={JSTOR}
}
@Article{Huelsenbeck2001a,
Title = {{MRBAYES: Bayesian inference of phylogenetic trees}},
Author = {Huelsenbeck, J.P. and Ronquist, F.},
Journal = {Bioinformatics},
Year = {2001},
Number = {8},
Pages = {754--755},
Volume = {17},
DOI = {10.1093/bioinformatics/17.8.754},
Owner = {shhn001},
Publisher = {Oxford Univ Press},
Timestamp = {2008.04.02}
}
@article{phylogenyio,
title = {Interactive web-based visualization of phylogenetic trees using Phylogeny.IO},
author = {Jovanovic, Nikola and Mikheyev, Alexander S},
year = {2016},
volume = {4},
pages = {e2579v1},
journal = {PeerJ Preprints},
issn = {2167-9843},
doi = {10.7287/peerj.preprints.2579v1},
}
@Article{Lewis2001,
Title = {{A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data}},
Author = {Lewis, Paul O.},
Journal = SYSBIO,
Year = {2001},
Number = {6},
Pages = {913-925},
Volume = {50},
DOI = {10.1080/106351501753462876},
Owner = {pett},
Publisher = {Oxford University Press},
Timestamp = {2016.12.23}
}
@Misc{Maddison2008,
Title = {Mesquite: a modular system for evolutionary analysis. Version 2.5},
Author = {Maddison, W. P. and Maddison, D. R.},
HowPublished = {http://mesquiteproject.org},
Year = {2008},
Owner = {shhn001},
Timestamp = {2009.01.12},
Url = {http://mesquiteproject.org}
}
@article{meir2007,
author = {Meir, E. Perry, J., Herron, J. C., and Kingsolver, J.},
title = {College Students' Misconceptions About Evolutionary Trees},
journal = {The American Biology Teacher},
volume = {69},
year = {2007},
doi = {10.1662/0002-7685(2007)69[71:csmaet]2.0.co;2}
}
@Article{Meisel2010,
author={Meisel, Richard P.},
title={Teaching Tree-Thinking to Undergraduate Biology Students},
journal={Evolution: Education and Outreach},
year={2010},
month={Dec},
day={01},
volume={3},
number={4},
pages={621--628},
issn={1936-6434},
doi={10.1007/s12052-010-0254-9},
url={10.1007/s12052-010-0254-9}
}
@article{ohara1997,
title={Population thinking and tree thinking in systematics},
author={O'Hara, Robert J},
journal={Zoologica Scripta},
volume={26},
number={4},
pages={323--329},
year={1997},
doi={10.1111/j.1463-6409.1997.tb00422.x},
publisher={Wiley Online Library}
}
@Manual{R,
Title = {R: A Language and Environment for Statistical Computing},
Address = {Vienna, Austria},
Author = {{R Core Team}},
Organization = {R Foundation for Statistical Computing},
Year = {2013},
Owner = {hoehna},
Timestamp = {2013.07.09},
Url = {http://www.R-project.org}
}
@Manual{RStudio,
title = {RStudio: Integrated Development Environment for {R}},
author = {{RStudio Team}}, organization = {RStudio, Inc.},
address = {Boston, MA},
year = {2015},
url = {http://www.rstudio.com/}
}
@article{rudolph1998,
title={Evolution and the nature of science: On the historical discord and its implications for education},
author={Rudolph, John L and Stewart, Jim},
journal={Journal of Research in Science Teaching: The Official Journal of the National Association for Research in Science Teaching},
volume={35},
number={10},
pages={1069--1089},
year={1998},
DOI={10.1002/(SICI)1098-2736(199812)35:10<1069::AID-TEA2>3.0.CO;2-A},
publisher={Wiley Online Library}
}
@article{sandvik2008,
title={Tree thinking cannot taken for granted: challenges for teaching phylogenetics},
author={Sandvik, Hanno},
journal={Theory in Biosciences},
volume={127},
number={1},
pages={45--51},
year={2008},
DOI={10.1007/s12064-008-0022-3},
publisher={Springer}
}
@article{icytree,
author = {Vaughan, T. G.},
title = {IcyTree: Rapid browser-based visualization for phlogenetic trees and networks},
journal = {Bioinformatics},
year = {2017},
pages = {315-328},
doi = {10.1093/bioinformatics/btx155}
}
@Book{ggplot2,
author = {Hadley Wickham},
title = {{g}gplot2: Elegant Graphics for Data Analysis},
publisher = {Springer-Verlag New York},
year = {2016},
isbn = {978-3-319-24277-4},
url = {https://ggplot2.tidyverse.org},
}
@Article{ggtree,
title = {{g}gtree: an {R} package for visualization and annotation of phylogenetic trees with their covariates and other associated data.},
author = {Guangchuang Yu and David Smith and Huachen Zhu and Yi Guan and Tommy Tsan-Yuk Lam},
year = {2017},
journal = {Methods in Ecology and Evolution},
volume = {8},
issue = {1},
pages = {28-36},
doi = {10.1111/2041-210X.12628},
url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract},
}