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1
Taming the BEAST—A Community Teaching Material Resource for BEAST 2
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2
Taming the BEAST—A Community Teaching Material Resource for BEAST 2
In: Ecology, Evolution and Organismal Biology Publications (2018)
Abstract: Phylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two fields have many practical applications in disciplines as diverse as epidemiology, developmental biology, palaeontology, ecology, and linguistics. The combination of increasingly large genetic data sets and increases in computing power is facilitating the development of more sophisticated phylogenetic and phylodynamic methods. Big data sets allow us to answer complex questions. However, since the required analyses are highly specific to the particular data set and question, a black-box method is not sufficient anymore. Instead, biologists are required to be actively involved with modeling decisions during data analysis. The modular design of the Bayesian phylogenetic software package BEAST 2 enables, and in fact enforces, this involvement. At the same time, the modular design enables computational biology groups to develop new methods at a rapid rate. A thorough understanding of the models and algorithms used by inference software is a critical prerequisite for successful hypothesis formulation and assessment. In particular, there is a need for more readily available resources aimed at helping interested scientists equip themselves with the skills to confidently use cutting-edge phylogenetic analysis software. These resources will also benefit researchers who do not have access to similar courses or training at their home institutions. Here, we introduce the “Taming the Beast” (https://taming-the-beast.github.io/) resource, which was developed as part of a workshop series bearing the same name, to facilitate the usage of the Bayesian phylogenetic software package BEAST 2.
Keyword: Behavior and Ethology; Computational Biology; Ecology and Evolutionary Biology; Systems Biology
URL: https://lib.dr.iastate.edu/eeob_ag_pubs/254
https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1257&context=eeob_ag_pubs
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3
Language phylogenies reveal expansion pulses and pauses in Pacific settlement
In: Science (2015)
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4
How accurate and robust are the phylogenetic estimates of Austronesian language relationships?
In: PLoS ONE (2015)
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5
How accurate and robust are the phylogenetic estimates of Austronesian language relationships?
In: PLoS ONE (2015)
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6
Language phylogenies reveal expansion pulses and pauses in Pacific settlement
In: Science (2015)
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7
Mapping the Origins and Expansion of the Indo-European Language Family
In: Science (2015)
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8
The unity of extraposition and the A/A' distinction
In: CLS 45-2 : the panels (2011), p. 43-56
MPI für Psycholinguistik
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9
Minimalist construal : two approaches to A and B
In: The Oxford handbook of linguistic minimalism (New York, 2011), p. 396-426
MPI für Psycholinguistik
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10
How Accurate and Robust Are the Phylogenetic Estimates of Austronesian Language Relationships?
Greenhill, Simon J.; Drummond, Alexei J.; Gray, Russell D.. - : Public Library of Science, 2010
BASE
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11
Bayesian evolutionary analysis by sampling trees : practice
In: The phylogenetic handbook (Cambridge, 2009), p. 576-591
MPI für Psycholinguistik
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12
Bayesian evolutionary analysis by sampling trees : theory
In: The phylogenetic handbook (Cambridge, 2009), p. 564-575
MPI für Psycholinguistik
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13
Language phylogenies reveal expansion pulses and pauses in Pacific settlement
In: Science. - Washington, DC : AAAS, American Assoc. for the Advancement of Science 323 (2009) 5913, 479-483
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