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.
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
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
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/
$ sudo make install
It may take a few minutes to finish. After that, you can easily use TREE-PUZZLE on your system.
- 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.
Tutorial: Constructing phylogenetic tree using MEGA7
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 . (more…)
Update: A multi-epitope in silico vaccine candidate designed for Covid-19
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…)
Phylogenetics analysis of SARS-CoV-2 spike glycoproteins
A novel coronavirus (CoV), named Severe Acute Respiratory Syndrome-CoV-2 (SARS-CoV-2) or nCoV-2019, has emerged since December 2019 from Wuhan city of Hubei province in China . This virus belongs to the coronavirus family from which previous outbreaks have emerged (SARS and MERS). They have been a great threat to public health causing many deaths including SARS-CoV-2. There is no proper treatment available to cure this coronavirus disease (covid19). Scientists and researchers are trying really hard to develop a drug or a vaccine or a proper way to cure covid19. (more…)