Tree compression

Simple prototype implementation of tree compression methods (a simple compression and a compression using the RF metric) in C / C++.

Getting Started

Download the repository, install the required libraries PLL modules and SLSL-lite. Once you have installed the two libraries, you can compile the project running

make

You then can run a simple compression on two trees with 500 taxa stored in the folder 500/ by running

./main ../data/500/tree_1.nwk ../data/500/tree_2.nwk

Also, you can change the trees by changing the number of the tree (e.g. using tree_10.nwk). There are 200 trees in the folder. Additionally, trees with 27 taxa are stored in 027/.

Prerequisites

To be able to run the tree compression, you will need to download and install the PLL modules

git clone https://github.com/ddarriba/pll-modules.git

as well as the SLSL library

git clone https://github.com/simongog/sdsl-lite.git

Authors

• Axel Trefzer - axeltref
• Alexis Stamatakis - Ideas and advice - stamatak
• Simon Gog - Initial ideas - simongog