<Plotting coalescent trees using R
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Plotting coalescent trees using R

Plotting coalescent trees using R (MAB scripts)

In order to work the scripts require two packages:

  • ape
  • phyclust

If they are not installed you need to open R and

  1. set Cran Mirror, and choose one e.g. Bristol/Toulouse/ (but not https)
  2. select repositories, and accept the default it suggests
  3. select packages, choose ape and also choose phyclust

Also, you can type:

install.packages(c("phyclust", "ape"))


There are two scripts:

Type:

source(“plot_ms_trees_single_pop.R”)

This will import the function plot_ms_tree() This function has two parameters:

  • The number of haploid samples
  • The ms options for a single pop

You can run different scenarios:

  • Standard stationary population. 
    plot_ms_tree(10, "-T")
  • Population growth. 
    plot_ms_tree(10, "-T -G 1000")
  • Population decrease. 
    plot_ms_tree(100,"-T -G -2.119 -eG 2.5 0.0")

The second script allows you to simulate structured populations and works differently

Type:

source(“plot_ms_trees_mig.R”)

It should plot a tree with two colors corresponding to two populations.

Open/Edit the ms command (change the migration rate for instance) and save your changes.

Type again:

source(“plot_ms_trees_mig.R”)


Plotting average trees using R (WR script)

There are two scripts:

Type:

source(“CoalTreesSimulation.R”)

Then you can open the file CoalTreesSimulation.R in a text editor and modify some of the parameters to see what happens.


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