# Difference between revisions of "Divergence Times"

From MolEvol

(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...") |
|||

(27 intermediate revisions by 2 users not shown) | |||

Line 1: | Line 1: | ||

+ | [[File:IMG 1313.jpg|thumb|right]] | ||

+ | |||

+ | Course materials by [[Tracy Heath]] on Bayesian Divergence Time Estimation (2013). | ||

+ | |||

+ | __NOTOC__ | ||

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

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

+ | |||

== Lab Practical: Divergence time estimation using BEAST == | == Lab Practical: Divergence time estimation using BEAST == | ||

=== Tutorial === | === Tutorial === | ||

− | |||

− | + | 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/] | |

− | |||

− | |||

− | |||

− | |||

− | |||

− | |||

=== Software === | === Software === | ||

Line 26: | Line 25: | ||

* [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) | ||

+ | |||

+ | |||

+ | == 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 [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] | ||

+ | * 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

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