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@article{Sanderson,
author = {Sanderson, M. J. and Baldwin, B. G. and Bharathan, G. and Campbell, C. S. and von Dohlen, C. and Ferguson, D. and Porter, J. M. and Wojciechowski, M. F. and Donoghue, M. J.},
title = {The Growth of Phylogenetic Information and the Need for a Phylogenetic Data Base},
journal = {Systematic Biology},
volume = 42,
number = 4,
pages = {562-568},
year = 1993,
url = {https://doi.org/10.1093/sysbio/42.4.562}
}
@incollection{Yates,
author = {Yates, T. L. and Salazar-Bravo, J. and Dragoo, J. W.},
title = {The Importance of knowing the Tree of Life},
editor = {Cracraft, J. and Donoghue, M. J.},
booktitle = {Assembling the Tree of Life},
publisher = {Oxford University Press},
address = {Oxford},
year = 2004,
pages = {7-17},
chapter = 1
}
@article{Cracraft,
title = {The Seven Great Questions of Systematic Biology: An Essential Foundation for Conservation and the Sustainable Use of Biodiversity},
journal = {Annals of the Missouri Botanical Garden},
volume = {89},
copyright = {In copyright. Digitized with the permission of the rights holder.},
url = {https://www.biodiversitylibrary.org/part/16378},
publisher = {St. Louis :Missouri Botanical Garden Press,1914-},
author = {Cracraft, J.},
year = {2002},
pages = {127--144}
}
@article{Piel,
author = {Piel, W. H. and Sanderson, M. J. and Donoghue, M. J.},
title = "{The small-world dynamics of tree networks and data mining in phyloinformatics}",
journal = {Bioinformatics},
volume = {19},
number = {9},
pages = {1162-1168},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/btg131}
}
@article{Maddison,
author = {Maddison, David R. and Swofford, David L. and Maddison, Wayne P.},
title = "{Nexus: An Extensible File Format for Systematic Information}",
journal = {Systematic Biology},
volume = {46},
number = {4},
pages = {590-621},
year = {1997},
url = {https://doi.org/10.1093/sysbio/46.4.590}
}
@article{Inglis,
title = "Fast and inexpensive protocols for consistent extraction of high
quality {DNA}and {RNA}from challenging plant and fungal
samples for high-throughput {SNP}genotyping and sequencing
applications",
author = "Inglis, Peter W and Pappas, Marilia de Castro R and Resende, Lucileide V and Grattapaglia, Dario",
journal = "PLoS One",
publisher = "Public Library of Science (PLoS)",
volume = 13,
number = 10,
pages = "e0206085",
month = oct,
year = 2018,
copyright = "http://creativecommons.org/licenses/by/4.0/",
language = "en"
}
@misc{wikiBioinformatics,
author = "{Wikipedia contributors}",
title = "Bioinformatics --- {Wikipedia}{,}The Free Encyclopedia",
year = "2022",
url = "https://en.wikipedia.org/w/index.php?title=Bioinformatics&oldid=1108690744",
note = "[Online; accessed 10-September-2022]"
}
@misc{wikiTim,
author = "{Wikipedia contributors}",
title = "Tim Berners-Lee --- {Wikipedia}{,}The Free Encyclopedia",
year = "2022",
url = "{https://pt.wikipedia.org/wiki/Tim{\_}Berners-Lee}",
note = "[Online; accessed 11-September-2022]"
}
@misc{wikiW3C,
author = "{Wikipedia contributors}",
title = "W3C --- {Wikipedia}{,}The Free Encyclopedia",
year = "2022",
url = "https://pt.wikipedia.org/wiki/W3C",
note = "[Online; accessed 11-September-2022]"
}
@misc{wikiGO,
author = "{Wikipedia contributors}",
title = "Gene Ontology --- {Wikipedia}{,}The Free Encyclopedia",
year = "2022",
url = "{https://en.wikipedia.org/wiki/Gene{\_}Ontology}",
note = "[Online; accessed 11-September-2022]"
}
@misc{wikiInteroperabilidadeSemantica,
author = "{Wikipedia contributors}",
title = "{Interoperabilidade sem\^{a}ntica --- {Wikipedia}{,}The Free Encyclopedia}",
year = "2022",
url = "{https://pt.m.wikipedia.org/wiki/Interoperabilidade{\_}sem{\%}C3{\%}A2ntica}",
note = "[Online; accessed 12-September-2022]"
}
@misc{wikiInteroperabilidade,
author = "{Wikipedia contributors}",
title = "Interoperabilidade --- Governo Digital",
year = "2022",
url = "{https://www.gov.br/governodigital/pt-br/governanca-de-dados/interoperabilidade}",
note = "[Online; accessed 12-September-2022]"
}
@misc{ePING,
author = "{Programa de Governo Eletr\^{o}nico Brasileiro}",
title = "{Padr\~oes de Interoperabilidade de Governo Eletr\^onico - ePING --- Vers\~ao 2018}",
year = "2022",
url = "https://eping.governoeletronico.gov.br",
note = "[Online; accessed 13-September-2022]"
}
@misc{WebEvolution,
author = "{Vivek Madurai}",
title = "Web Evolution from 1.0 to 3.0",
year = "2018",
url = "{https://medium.com/@vivekmadurai/web-evolution-from-1-0-to-3-0-e84f2c06739}",
note = "[Online; accessed 13-September-2022]"
}
@misc{wikiCibernetica,
author = "{Wikipedia contributors}",
title = "{Cibern\'{e}tica --- Governo Digital}",
year = "2022",
url = "{https://pt.wikipedia.org/wiki/Cibern{\%}C3{\%}A9tica}",
note = "[Online; accessed 12-September-2022]"
}
@article{TrendsandPriorities,
author = {An\{^}onimo},
title = "{Trends, Priorities, and Needs in Systematic and Evolutionary Biology}",
journal = {Systematic Biology},
volume = {23},
number = {3},
pages = {416-439},
year = {1974},
url = {https://doi.org/10.1093/sysbio/23.3.416}
}
@article{Eshbaugh,
author = {Eshbaugh, W. H.},
title = {Systematics Agenda 2000: an historical perspective},
journal = {Biodiversity & Conservation},
volume = 4,
number = 5,
pages = {455-462},
year = 1995,
url = {https://doi.org/10.1007/BF00056336}
}
@article{Cracraft,
title = {The Seven Great Questions of Systematic Biology: An Essential Foundation for Conservation and the Sustainable Use of Biodiversity},
journal = {Annals of the Missouri Botanical Garden},
volume = {89},
copyright = {In copyright. Digitized with the permission of the rights holder.},
url = {https://www.biodiversitylibrary.org/part/16378},
publisher = {St. Louis :Missouri Botanical Garden Press,1914-},
author = {Cracraft, J.},
year = {2002},
pages = {127--144},
}
@article{Cornish-Bowden,
author = {Cornish-Bowden, A.},
title = "{Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984}",
journal = {Nucleic Acids Research},
volume = {13},
number = {9},
pages = {3021-3030},
year = {1985},
url = {https://doi.org/10.1093/nar/13.9.3021}
}
@article{Hall,
author = {Hall, T. A.},
title = {BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT},
journal = {Nucleic Acids Symposium Series},
volume = 41,
number = {},
pages = {95-98},
year = 1999
}
@article{Muller,
author = {M\"{u}ller, K.},
title = {SeqState: Primer Design and Sequence Statistics for Phylogenetic DNA Datasets},
journal = {Applied Bioinformatics},
volume = 4,
number = 1,
pages = {65-69},
year = 2005,
url = {https://doi.org/10.2165/00822942-200504010-00008}
}
@article{Vaidya,
author = {Vaidya, G. and Lohman, D. J. and Meier, R.},
title = {SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information},
journal = {Cladistics},
volume = 27,
number = 2,
pages = {171-180},
year = 2011,
url = {https://doi.org/10.1111/j.1096-0031.2010.00329.x}
}
@article{Huson,
author = {Huson, Daniel H. and Bryant, David},
title = "{Application of Phylogenetic Networks in Evolutionary Studies}",
journal = {Molecular Biology and Evolution},
volume = {23},
number = {2},
pages = {254-267},
year = {2005},
url = {https://doi.org/10.1093/molbev/msj030}
}
@article{Huelsenbeck,
author = {Huelsenbeck, John P. and Ronquist, Fredrik},
title = "{MRBAYES: Bayesian inference of phylogenetic trees}",
journal = {Bioinformatics},
volume = {17},
number = {8},
pages = {754-755},
year = {2001},
url = {https://doi.org/10.1093/bioinformatics/17.8.754}
}
@article{Doyles1987,
title={A rapid DNA isolation procedure for small quantities of fresh leaf tissue},
author={Doyle, J.J. and Doyle, J.L.},
journal={Phytochemical Bulletin},
year={1987},
volume={19},
pages={11-15}
}
@article{Hagemann1999,
url = {https://doi.org/10.1385/mb:13:2:137},
year = {1999},
publisher = {Springer Science and Business Media {LLC}},
volume = {13},
number = {2},
pages = {137--152},
author = {Tracy L. Hagemann and Sau-Ping Kwan},
title = {{ABI} Sequencing Analysis: Manipulation of Sequence Data from the {ABI}{DNA}Sequencer},
journal = {Molecular Biotechnology}
}
@misc{wikiXML,
author = "{Wikipedia contributors}",
title = "XML --- {Wikipedia}{,}The Free Encyclopedia",
year = "2022",
url = "https://pt.wikipedia.org/wiki/XML",
note = "[Online; accessed 15-September-2022]"
}
@article{Souza_Alvarenga_2004,
author = {Souza, R.R. and Alvarenga, L.},
title = {A Web Sem\^{a}ntica e suas contribui\c{c}\~{o}es para a ci\^{e}ncia da informa\c{c}\~{a}o},
journal = {Ci. Inf., Bras\'{\i}lia},
volume = 33,
number = 1,
pages = {132--141},
year = 2004
}
@article{Almeida_2002,
author = {Almeida, M.B.},
title = {Uma introdu\c{c}\~{a}o ao XML, sua utiliza\c{c}\~{a}o na Internet e alguns conceitos complementares},
journal = {Ci. Inf., Bras\'{\i}lia},
volume = 31,
number = 2,
pages = {5--13},
year = 2002
}
@article{Gastauer2017,
url = {https://doi.org/10.1590/0102-33062016abb0306},
year = {2017},
volume = {31},
number = {2},
pages = {191--198},
author = {Markus Gastauer and Jo\~{a}o Augusto Alves Meira Neto},
title = {Updated angiosperm family tree for analyzing phylogenetic diversity and community structure},
journal = {Acta Botanica Brasilica}
}
@article{Li2021,
url = {https://doi.org/10.1186/s12915-021-01166-2},
year = {2021},
volume = {19},
number = {1},
author = {Hong-Tao Li and Yang Luo and Lu Gan and Peng-Fei Ma and Lian-Ming Gao and Jun-Bo Yang and Jie Cai and Matthew A. Gitzendanner and Peter W. Fritsch and Ting Zhang and Jian-Jun Jin and Chun-Xia Zeng and Hong Wang and Wen-Bin Yu and Rong Zhang and Michelle van der Bank and Richard G. Olmstead and Peter M. Hollingsworth and Mark W. Chase and Douglas E. Soltis and Pamela S. Soltis and Ting-Shuang Yi and De-Zhu Li},
title = {Plastid phylogenomic insights into relationships of all flowering plant families},
journal = {{BMC} Biology}
}
@article{Johnson2018,
url = {https://doi.org/10.1093/sysbio/syy086},
year = {2018},
volume = {68},
number = {4},
pages = {594--606},
author = {Matthew G Johnson and Lisa Pokorny and Steven Dodsworth and Laura R Botigu\'e and Robyn S Cowan and Alison Devault and Wolf L Eiserhardt and Niroshini Epitawalage and F{\'{e}}lix Forest and Jan T Kim and James H Leebens-Mack and Ilia J Leitch and Olivier Maurin and Douglas E Soltis and Pamela S Soltis and Gane Ka-shu Wong and William J Baker and Norman J Wickett},
editor = {Susanne Renner},
title = {A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering},
journal = {Systematic Biology}
}
@misc{wikiCirculoViena,
author = "{Wikipedia contributors}",
title = "C\'{\i}rculo de Viena --- {Wikipedia}{,}The Free Encyclopedia",
year = "2022",
url = "https://pt.wikipedia.org/wiki/C{\%}C3{\%}ADrculo_de_Viena",
note = "[Online; accessed 15-September-2022]"
}
@article{Luz2014,
url = {https://doi.org/10.4000/sociologico.1007},
year = {2014},
volume = {24},
pages = {27--32},
author = {Madel T. Luz},
title = {Impactos da tecnoci\^{e}ncia nos saberes, na cultura da vida e sa\'{u}de},
journal = {Forum Sociol\'{o}gico}
}
@article{Santos_Klassa2012,
url = {https://doi.org/10.1590/S1678-31662012000300008},
year = {2012},
number = {3},
volume = 10,
pages = {593--612},
author = {Santos, Charles Morphy Dias and Klassa, Bruna},
title = {Sistem\'{a}tica filogen\'{e}tica hennigiana: revolu\c{c}\~{a}o ou mudan\c{c}a no interior de um paradigma?},
journal = {Scientiae Studia [online]}
}
@article{Santos2008,
url = {https://doi.org/10.1590/S1678-31662008000200003},
year = {2008},
number = 6,
volume = 2,
pages = {179--200},
author = {Santos, Charles Morphy Dias},
title = {Os dinossauros de Hennig: sobre a import\^{a}ncia do monofiletismo para a sistem\'{a}tica biol\'{o}gica},
journal = {Scientiae Studia [online]}
}
@Thesis{Terra2010,
url = {http://www.uesc.br/eventos/ivseminariohfc/resumos/otriunfodacladistica.pdf},
date = {2010},
author = {Paulo S. Terra},
institution = {Bahia: Universidade Estadual de Santa Cruz},
title = {O triunfo da clad\'{\i}stica: a an\'{a}lise do embate te\'{o}rico ocorrido na sistem\'{a}tica biol\'{o}gica na segunda metade do s\'{e}culo xx},
type = {IV Semin\'{a}rio de Hist\'{o}ria e Filosofia da Ci\^{e}ncia}
}
@book{Mayr1982,
title={The Growth of Biological Thought: Diversity, Evolution, and Inheritance},
author={Ernst Mayr},
year={1982},
publisher = "Harvard University Press",
address = "Cambridge, MA"
}
@article{Tremblay2013,
url = {https://doi.org/10.1007/s13752-012-0077-8},
year = {2013},
volume = {7},
number = {1},
pages = {56--68},
author = {Frederic Tremblay},
title = {Nicolai Hartmann and the Metaphysical Foundation of Phylogenetic Systematics},
journal = {Biological Theory}
}
@book{Schmitt2013,
title = "From Taxonomy to Phylogenetics - Life and Work of Willi Hennig",
author = "Schmitt, M.",
year = 2013,
publisher = "Brill",
address = "Leiden; Boston"
}
@article{Mattox2011,
url = {https://doi.org/10.7594/revbio.07.09},
year = {2011},
publisher = {Universidade de Sao Paulo, Agencia {USP} de Gestao da Informacao Academica ({AGUIA})},
volume = {7},
pages = {49--55},
author = {George M. T. Mattox},
title = {Gareth Nelson: os desafios atuais e o futuro da biogeografia.},
journal = {Revista da Biologia}
}
@article{Nelson1974,
url = {https://doi.org/10.1093/sysbio/23.3.452},
year = {1974},
volume = {23},
number = {3},
pages = {452--458},
author = {G. Nelson},
title = {Darwin-Henning Classification: A Reply to Ernst Mayr},
journal = {Systematic Biology}
}
@article{Eldredge2010,
url = {https://doi.org/10.1007/s12052-010-0284-3},
year = {2010},
volume = {3},
number = {4},
pages = {491--494},
author = {Niles Eldredge},
title = {How Systematics Became {\textquotedblleft}Phylogenetic{\textquotedblright}},
journal = {Evolution: Education and Outreach}
}
@article{Felsenstein1981,
url = {https://doi.org/10.1007/bf01734359},
year = {1981},
volume = {17},
number = {6},
pages = {368--376},
author = {Joseph Felsenstein},
title = {Evolutionary trees from {DNA} sequences: A maximum likelihood approach},
journal = {Journal of Molecular Evolution}
}
@article{Holland2013,
url = {https://doi.org/10.1111/anzs.12035},
year = {2013},
volume = {55},
number = {3},
pages = {205--220},
author = {Barbara R. Holland},
title = {The Rise of Statistical Phylogenetics},
journal = {Australian {\&}amp$\mathsemicolon$ New Zealand Journal of Statistics}
}
@article{Posada2021,
url = {https://doi.org/10.1007/s00239-020-09982-w},
year = {2021},
volume = {89},
number = {3},
pages = {134--145},
author = {David Posada and Keith A. Crandall},
title = {Felsenstein Phylogenetic Likelihood},
journal = {Journal of Molecular Evolution}
}
@incollection{Patterson1982,
author = {Patterson, C.},
title = {Morphological characters and homology},
editor = {Joysey, K.A. and Friday, A.E.},
booktitle = {Problems of Phylogenetic Reconstruction},
publisher = {Academic Press},
address = {New York, NY},
year = 1982,
pages = {21--74},
chapter = 1
}
@article{Pinna1991,
url = {https://doi.org/10.1111/j.1096-0031.1991.tb00045.x},
year = {1991},
volume = {7},
number = {4},
pages = {367--394},
author = {Mario C. C. Pinna},
title = {Concepts and tests of homology in the cladistic paradigm},
journal = {Cladistics}
}
@article{Brower2012,
url = {https://doi.org/10.1111/j.1096-0031.2012.00398.x},
year = {2012},
volume = {28},
number = {5},
pages = {529--538},
author = {Andrew V.Z. Brower and Mario C.C. de Pinna},
title = {Homology and errors},
journal = {Cladistics}
}
@misc{wikiFrege,
author = "{Wikipedia contributors}",
title = "Gottlob Frege --- {Wikipedia}{,}The Free Encyclopedia",
year = "2022",
url = "https://pt.wikipedia.org/wiki/Gottlob_Frege",
note = "[Online; accessed 23-September-2022]"
}
@misc{wikiRussell,
author = "{Wikipedia contributors}",
title = "Bertrand Russell --- {Wikipedia}{,}The Free Encyclopedia",
year = "2022",
url = "https://pt.wikipedia.org/wiki/Bertrand_Russell",
note = "[Online; accessed 23-September-2022]"
}