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Phylogenetics

Installing TREE-PUZZLE on Ubuntu

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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

  1. Schmidt, H. A., Strimmer, K., Vingron, M., & Von Haeseler, A. (2002). TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics18(3), 502-504.
  2. Schmidt, H. A., & von Haeseler, A. (2007). Maximum‐likelihood analysis using TREE‐PUZZLE. Current Protocols in Bioinformatics17(1), 6-6.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

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