BIOSCI 700: Phylogenetics

Required Software

Java 17 or higher (Install it, only if it is not available in your machine)
BEAST 2.7.7 http://www.beast2.org
Tracer 1.7.2 https://github.com/beast-dev/tracer/releases
To visualize the tree, you may use FigTree 1.4.4 or icytree if you prefer a software with a GUI, or ggtree if you prefer R.
Beagle (optional): this is a high-performance library that can perform the core calculations at the heart of most Bayesian and maximum likelihood phylogenetics packages. https://github.com/beagle-dev/beagle-lib/wiki

Required BEAST 2 packages

Use Package Manager to install all required packages:

Assignments

Useful links

R examples or R tutorial, and R tutorial for vectorisation
Math in R markdown
More R markdown
IcyTree
FigTree
BEAST 2

3rd party software issues

Resize a image in a .Rmd file in RStudio

![Q2](./tree2t.png) may result in a large size when creating HTML from the .Rmd file. You may consider using the following code to replace it, which allows you to add a resized image:

<img src="tree2t.png" alt="Q2" width="200"/>

Mac version issues

Cannot be opened

The latest version of macOS has implemented stricter security protocols for opening downloaded software. As a result, you may encounter the following error on a Mac:

Cannotbeopened

To resolve the issue, navigate to “System Settings” => “Privacy & Security” => “Security” on your Mac, and select “Allow Anyway” for the software in question.

MacAllowIqtree2

Afterwards, relaunch the application (for instance, iqtree2). When prompted, click “Open” in the pop-up window to proceed.

MacRunIqtree2Open

Incorrectly prompt for the installation of Java 1.6

Note that the Mac version of TempEst and FigTree may have an issue where they incorrectly prompt for the installation of Java 1.6. This is a known bug and does not affect the functionality of the programs. To run FigTree or TempEst, you can simply extract and launch the executable version (e.g., FigTree_v1.4.4.tgz) without needing to install Java 1.6 separately.

To start FigTree, run the following command in the terminal:

bash cd /Applications/FigTree1.4.4 bin/figtree

If figtree is not executable in your machine, run the following command in the terminal before starting FigTree:

bash chmod u+x bin/figtree