Difference between revisions of "Divergence Times"

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(Created page with "== Lecture == Bayesian methods for dating species divergences ([https://molevol.mbl.edu/wiki/images/6/6e/WHME_2012_lecture.pdf slides]) == Lab Practical: Divergence time est...")
 
 
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[[File:IMG 1313.jpg|thumb|right]]
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Course materials by [[Tracy Heath]] on Bayesian Divergence Time Estimation (2013).
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__NOTOC__
 
== Lecture ==  
 
== Lecture ==  
Bayesian methods for dating species divergences ([https://molevol.mbl.edu/wiki/images/6/6e/WHME_2012_lecture.pdf slides])
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Bayesian methods for dating species divergences: [[media:WH_2013_lecture.pdf‎ | slides]] (#molevol2013 version)
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== Lab Practical: Divergence time estimation using BEAST ==
 
== Lab Practical: Divergence time estimation using BEAST ==
  
 
=== Tutorial ===
 
=== Tutorial ===
* Detailed tutorial [https://molevol.mbl.edu/wiki/images/f/ff/WHME_12_BEAST_tutorial.pdf PDF] (final version...I think)
 
  
=== Data and Output Files ===
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The detailed tutorial and data files can be found here: [http://treethinkers.org/divergence-time-estimation-using-beast/ http://treethinkers.org/divergence-time-estimation-using-beast/]  
Downloads:
 
* [https://molevol.mbl.edu/wiki/images/f/fc/Whme_beast_data.tar.gz Data files]
 
* Output files
 
** [https://molevol.mbl.edu/wiki/images/d/d8/Whme_beast_output1.tar.gz output 1]
 
** [https://molevol.mbl.edu/wiki/images/d/db/Whme_beast_output2.tar.gz output 2]
 
** [https://molevol.mbl.edu/wiki/images/b/ba/Whme_beast_output3.tar.gz output 3]
 
  
 
=== Software ===
 
=== Software ===
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* [http://packages.python.org/DendroPy/ DendroPy] (*optional)
 
* [http://packages.python.org/DendroPy/ DendroPy] (*optional)
 
* [http://bodegaphylo.wikispot.org/starttree_program starttree] (*optional)
 
* [http://bodegaphylo.wikispot.org/starttree_program starttree] (*optional)
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== Optional Tutorials: Phylodynamics of Infectious Diseases ==
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Many students are interested in Bayesian methods for understanding epidemiology. There are some great tools for applying these methods, including BEAST2:
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* Alexei Drummand & Remco Bouckaert's [http://beast2.cs.auckland.ac.nz/index.php/Main_Page BEAST2] tutorial on: [http://beast2.googlecode.com/files/MEPsv2.0.2.pdf Measurably evolving populations, estimating rates, and Bayesian skyline plots]
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* Trevor Bedford's tutorial on (using BEAST1): [https://github.com/trvrb/influenza-dynamics-practical Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data]

Latest revision as of 07:36, 27 July 2013

IMG 1313.jpg

Course materials by Tracy Heath on Bayesian Divergence Time Estimation (2013).


Lecture

Bayesian methods for dating species divergences: slides (#molevol2013 version)


Lab Practical: Divergence time estimation using BEAST

Tutorial

The detailed tutorial and data files can be found here: http://treethinkers.org/divergence-time-estimation-using-beast/

Software


Optional Tutorials: Phylodynamics of Infectious Diseases

Many students are interested in Bayesian methods for understanding epidemiology. There are some great tools for applying these methods, including BEAST2: