Difference between revisions of "Tracy Heath"

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Assistant Professor<br/>
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Dept. Ecology, Evolution, & Organismal Biology<br/>
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Iowa State University
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__NOTOC__
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== Contact Information ==
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*Web page: http://phyloworks.org/
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*Twitter: [https://twitter.com/trayc7 @trayc7]
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*Email: phylo "at" iastate "dot" edu
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== Research ==
 
[[File:heath.jpg|thumb|right]]
 
[[File:heath.jpg|thumb|right]]
[[File:Ddday.JPG|thumb|right]]
 
  
'''Institutional home pages'''
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I develop statistical models for use as priors in Bayesian methods for phylogenetic inference. In particular, I'm interested in divergence-time estimation -- e.g. modeling rate variation across the tree of life, diversification processes, and methods for incorporating information from the fossil record.
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== Time at MBL ==
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Thursday August 1 - Sunday August 11
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== 2019 Course ==
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Divergence Time Estimation in RevBayes - August 4 & 5
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All workshop materials will be made available on the RevBayes website: https://revbayes.github.io/workshops/woodshole2019.html
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http://phylo.bio.ku.edu/content/tracy-heath
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== Suggested Reading ==
  
http://cteg.berkeley.edu/members/heath.html
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Graphical Models
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* Höhna, Heath, Boussau, Landis, Ronquist, Huelsenbeck. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology, 63:753–771. ([http://sysbio.oxfordjournals.org/content/63/5/753 doi: 10.1093/sysbio/syu039]).
  
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Divergence-Time Estimation
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* Thorne and Kishino. 2005. Estimation of divergence times from molecular sequence data. In: Nielsen R, editor, Statistical Methods in Molecular Evolution. New York: Springer, pp. 235–256. ([ftp://statgen.ncsu.edu/pub/thorne/mypapers/clockreview1215wfigs.pdf PDF])
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* Heath and Moore. 2014. Bayesian inference of species divergence times. In: Bayesian Phylogenetics: Methods, Algorithms, and Applications. Chen, M.-H., L. Kuo, and P.O. Lewis (editors). Chapman & Hall/CRC. (book chapter email me for PDF)
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* BEAST2 Book: Drummond AJ, Bouckaert RR. 2014. Bayesian evolutionary analysis with BEAST 2. Cambridge University Press. (http://www.beast2.org/book.html)
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* Lartillot: blog post on diversification: http://bayesiancook.blogspot.com/2013/12/two-sides-of-same-coin.html
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* also see references in [http://treethinkers.org/wp-content/uploads/2014/08/DivTime_BEAST2_tutorial_2014.pdf divergence-time tutorial]
  
== Time at MBL ==
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== Additional Tutorials ==
Sunday July 22 - Wednesday August 1
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* More tutorials on divergence time estimation in RevBayes and BEAST2 ([http://phyloworks.org/workshops/divtime.html link])
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* Materials (tutorials and lectures) from the Taming the BEAST workshop, including some tutorials on infectious disease dynamics ([https://www.bsse.ethz.ch/cevo/taming-the-beast/materials.html link])
  
== Lecture ==  
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== 2016 Course ==
Bayesian methods for dating species divergences
 
  
== Lab Practical: Divergence time estimation using BEAST ==
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* Phylogenetic Inference using [[RevBayes]] (with [[Michael Landis]])
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* [http://phyloworks.org/workshops/divtime.html Bayesian Divergence Time Estimation in BEAST2] ([http://phyloworks.org/workshops/WH_2015_divtime_lec_d.pdf slides])
  
=== Tutorial ===
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== 2017 Course ==
* Detailed tutorial PDF
 
  
=== Data and Output Files ===
 
  Downloads:
 
  * [https://molevol.mbl.edu/wiki/index.php/File:Whme_beast_data.tar.gz Data files]
 
  * Output files
 
  ** [https://molevol.mbl.edu/wiki/index.php/File:Whme_beast_output1.tar.gz output 1]
 
  ** [https://molevol.mbl.edu/wiki/index.php/File:Whme_beast_output2.tar.gz output 2]
 
  ** [https://molevol.mbl.edu/wiki/index.php/File:Whme_beast_output3.tar.gz output 3]
 
  
=== Software ===
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Morning lecture slides and example scripts
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* Hierarchical models and integrative Bayesian analysis ([https://www.slideshare.net/trayc7/integrative-bayesian-analysis-in-revbayes slides])
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** RevBayes archery model demo ([[:File:Archery_model.zip|files]])
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** RevBayes GTR demo ([https://github.com/revbayes/revbayes_tutorial/tree/master/RB_CTMC_Tutorial files])
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* Bayesian divergence-time estimation ([https://www.slideshare.net/trayc7/bayesian-divergence-time-estimation-lecture-at-bodega-2014-workshop slides])
  
* [http://beast.bio.ed.ac.uk/Main_Page BEAST] - software package includes:
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Afternoon tutorial
** BEAST
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* [[Total-evidence analysis in RevBayes]]
** BEAUti
 
** LogCombiner
 
** TreeAnnotator
 
* [http://tree.bio.ed.ac.uk/software/figtree/ FigTree]
 
* [http://tree.bio.ed.ac.uk/software/tracer/ Tracer]
 
* [http://packages.python.org/DendroPy/ DendroPy] (*optional)
 
* [http://bodegaphylo.wikispot.org/starttree_program starttree] (*optional)
 

Latest revision as of 14:31, 3 August 2019

Thsquare.jpg

Assistant Professor
Dept. Ecology, Evolution, & Organismal Biology
Iowa State University


Contact Information

Research

Heath.jpg

I develop statistical models for use as priors in Bayesian methods for phylogenetic inference. In particular, I'm interested in divergence-time estimation -- e.g. modeling rate variation across the tree of life, diversification processes, and methods for incorporating information from the fossil record.


Time at MBL

Thursday August 1 - Sunday August 11

2019 Course

Divergence Time Estimation in RevBayes - August 4 & 5

All workshop materials will be made available on the RevBayes website: https://revbayes.github.io/workshops/woodshole2019.html


Suggested Reading

Graphical Models

  • Höhna, Heath, Boussau, Landis, Ronquist, Huelsenbeck. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology, 63:753–771. (doi: 10.1093/sysbio/syu039).

Divergence-Time Estimation

  • Thorne and Kishino. 2005. Estimation of divergence times from molecular sequence data. In: Nielsen R, editor, Statistical Methods in Molecular Evolution. New York: Springer, pp. 235–256. (PDF)
  • Heath and Moore. 2014. Bayesian inference of species divergence times. In: Bayesian Phylogenetics: Methods, Algorithms, and Applications. Chen, M.-H., L. Kuo, and P.O. Lewis (editors). Chapman & Hall/CRC. (book chapter email me for PDF)
  • BEAST2 Book: Drummond AJ, Bouckaert RR. 2014. Bayesian evolutionary analysis with BEAST 2. Cambridge University Press. (http://www.beast2.org/book.html)
  • Lartillot: blog post on diversification: http://bayesiancook.blogspot.com/2013/12/two-sides-of-same-coin.html
  • also see references in divergence-time tutorial

Additional Tutorials

  • More tutorials on divergence time estimation in RevBayes and BEAST2 (link)
  • Materials (tutorials and lectures) from the Taming the BEAST workshop, including some tutorials on infectious disease dynamics (link)

2016 Course

2017 Course

Morning lecture slides and example scripts

  • Hierarchical models and integrative Bayesian analysis (slides)
    • RevBayes archery model demo (files)
    • RevBayes GTR demo (files)
  • Bayesian divergence-time estimation (slides)

Afternoon tutorial