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.
Previously, we have provided an installation tutorial for IQ-TREE on Ubuntu. In this article, we are going to perform model selection for a dataset using the standalone tool of IQ-TREE. (more…)
MEGAX is a bioinformatics software/tool used for phylogenetic tree construction. In this article, we will construct a maximum likelihood (ML) tree for a number of protein sequences using MEGA7 [1]. (more…)
Covid19 has created a great threat to human health. As you are aware, in this coronavirus outbreak, Bioinformatics Review has created a group, BiR-nCov19 Drug Development Team, to work on finding prevention to this disease. This research group consists of researchers from all over the world. (more…)
You must be logged in to post a comment Login