Phylodynamics activity

Table of contents

Lecture slides

  1. Uncovering macro-evolutionary dynamics based on genetic sequence data
  2. Uncovering epidemiological dynamics based on genetic sequence data

 

Expected learning outcome

In these exercises, you will learn how to use existing phylogenies to investigate diversification rates with the R packages TreePar and TreeSim.

 

Getting started

Just like the Geiger activities, the phylodynamics activities will be run using the R environment and can be run either on your own machine or on the Amazon Machine Image (AMI). If you have the R console or RStudio installed on your computer, we recommend that you use these tools. If using the AMI, please log in to it with ssh or PuTTY, create an activity directory, move into it, and start R with these commands

mkdir wme_jan2015/activities/Phylodynamics

cd wme_jan2015/activities/Phylodynamics

R

If you are running these exercises on your own computer, the R packages TreePar and TreeSim may not be installed yet. To test whether this is the case, start R and type

library(TreePar)

and

library(TreeSim)

If necessary, install both packages with

install.packages(“TreePar”, dependencies=T)

and

install.packages(“TreeSim”, dependencies=T)

(due to formatting problems with the double quotes, copy-paste will not work)

 

Exercise 1: Macroevolution

Please download the below script to either your computer or to the AMI using wget. We will discuss its functions as a group.

  1. Script: 01-Macroevolution.R

    You can download this file to your AMI with

    wget https://raw.githubusercontent.com/cevo-public/2015-CeskyKrumlov-Phylodynamics/master/01-Macroevolution.R

 

Exercise 2: Ebola

Please download the below scripts to either your computer or to the AMI using wget. We will discuss its functions as a group.

  1. Script: 02-Ebola.R

    You can download this file to your AMI with

    wget https://raw.githubusercontent.com/cevo-public/2015-CeskyKrumlov-Phylodynamics/master/02-Ebola.R

  2. Script: 02-Ebola-Functions.R

    This file should be saved in the same directory as 02-Ebola.R. You can download this file to your AMI with

    wget https://raw.githubusercontent.com/cevo-public/2015-CeskyKrumlov-Phylodynamics/master/02-Ebola-Functions.R

  3. Input file: 02-EbolaTrees.trees

    This file should be saved in the same directory as 02-Ebola.R. You can download this file to your AMI with

    wget https://raw.githubusercontent.com/cevo-public/2015-CeskyKrumlov-Phylodynamics/master/02-EbolaTrees.trees

  4. Answers: 02-Ebola-AnswersToQuestions.R

    You can download this file to your AMI with

    wget https://raw.githubusercontent.com/cevo-public/2015-CeskyKrumlov-Phylodynamics/master/02-Ebola-AnswersToQuestions.R

 

Exercise 3: Ebola in BEAST2

In this exercise, we will use BEAST2 to analyse a set of sequences of the 2014 Ebola outbreak. Please download the below guidelines and input files to either your computer or to the AMI using wget.

  1. Guidelines: EBOV_Setup.rtf

    You can download this file to your AMI with

    wget https://raw.githubusercontent.com/cevo-public/2015-CeskyKrumlov-Phylodynamics/master/03-EbolaInBeast/EBOV_Setup.rtf

    It can be opened in a rich text reader like Preview (on a OSX) or Notepad (on Windows).

  2. Input file: EBOV_2014_SL_SRD_SimpleRun.xml

    You can download this file to your AMI with

    wget https://github.com/cevo-public/2015-CeskyKrumlov-Phylodynamics/blob/master/03-EbolaInBeast/EBOV_2014_SL_SRD_SimpleRun.xml?raw=true

  3. Input file: EBOV_2014_SL_SRD_SimpleRunPrior.xml

    You can download this file to your AMI with

    wget https://github.com/cevo-public/2015-CeskyKrumlov-Phylodynamics/blob/master/03-EbolaInBeast/EBOV_2014_SL_SRD_SimpleRunPrior.xml?raw=true

  4. Input file: EBOV_2014_SL_SRD_SimpleRunPrior.xml

    You can download this file to your AMI with

    wget https://github.com/cevo-public/2015-CeskyKrumlov-Phylodynamics/blob/master/03-EbolaInBeast/EBOV_2014_SL_SRD_raw.xml?raw=true