Phylogenetics
Installing TREE-PUZZLE on Ubuntu
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.
References
- 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.
- Schmidt, H. A., & von Haeseler, A. (2007). Maximum‐likelihood analysis using TREE‐PUZZLE. Current Protocols in Bioinformatics, 17(1), 6-6.
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