Connect with us

Phylogenetics

Installing TREE-PUZZLE on Ubuntu

Dr. Muniba Faiza

Published

on

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

Phylogenetics

Tutorial: Constructing phylogenetic tree using MEGA7

Tariq Abdullah

Published

on

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 [1]. (more…)

Continue Reading

Phylogenetics

Update: A multi-epitope in silico vaccine candidate designed for Covid-19

Dr. Muniba Faiza

Published

on

covid19-vaccine

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…)

Continue Reading

Phylogenetics

Phylogenetics analysis of SARS-CoV-2 spike glycoproteins

Dr. Muniba Faiza

Published

on

Phylogenetic Tree of Covid Corona Virus with other Species

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 [1]. 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…)

Continue Reading

LATEST ISSUE

ADVERT