# Difference between revisions of "Divergence Times"

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== Lecture == | == Lecture == | ||

Bayesian methods for dating species divergences: [[media:WH_2013_lecture.pdf | slides]] (#molevol2013 version) | 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 == | ||

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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/] | 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/] | ||

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=== 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 == | == Optional Tutorials: Phylodynamics of Infectious Diseases == |

## Revision as of 07:36, 27 July 2013

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

- BEAST - software package includes:
- BEAST
- BEAUti
- LogCombiner
- TreeAnnotator

- FigTree
- Tracer
- DendroPy (*optional)
- starttree (*optional)

## 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:

- Alexei Drummand & Remco Bouckaert's BEAST2 tutorial on: Measurably evolving populations, estimating rates, and Bayesian skyline plots
- Trevor Bedford's tutorial on (using BEAST1): Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data