TREE-PUZZLE is a software to reconstruct phylogenetic trees using the maximum likelihood method [1,2]. It requires sequence data as input and implements a fast search algorithm and quartet puzzling. It can process large datasets easily. In this article, we will install TREE-PUZZLE on Ubuntu.

Preparing system

Let’s update and upgrade the system first.

Open the terminal (Ctrl+T) and type the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading TREE-PUZZLE

You can download the latest version of TREE-PUZZLE from here or use the following commands.

Move inside the directory where you want to download the software. Let’s say, ‘Downloads‘.

$ cd Downloads/

$ wget http://www.tree-puzzle.de/tree-puzzle-5.3.rc16-linux.tar.gz

Installing TREE-PUZZLE

Extract the file and then install.

$ tar xvzf tree-puzzle-5.3.rc16-linux.tar.gz

It will create a directory namely, ‘tree-puzzle-5.3.rc16-linux‘, now move inside this new directory and install using the following commands:

$ cd tree-puzzle-5.3.rc16-linux/

$ ./configure

$ make

$ sudo make install

It may take a few minutes to finish. After that, you can easily use TREE-PUZZLE on your system.

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References

1. Schmidt, H. A., Strimmer, K., Vingron, M., & Von Haeseler, A. (2002). TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics, 18(3), 502-504.
2. Schmidt, H. A., & von Haeseler, A. (2007). Maximum‐likelihood analysis using TREE‐PUZZLE. Current Protocols in Bioinformatics, 17(1), 6-6.