Connect with us

Software

How to install IQ-TREE on Ubuntu (Linux)?

Published

on

How to install IQ-TREE on Ubuntu (Linux)?

IQ-TREE [1] is a bioinformatics software for phylogenetic/phylogenomic inference. It is available as a webserver and a standalone tool. In this article, we are going to install IQ-TREE on Ubuntu.

Preparing system

Open a terminal by pressing Ctrl+Alt+T. Update and upgrade your system using the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading IQ-TREE

Let’s change to a directory where you want to download the software. We are downloading in ‘Downloads‘.

$ cd Downloads/

To download the software either visit this page or paste the following commands. We are installing stable version 1.6.12 of IQ-TREE for 64-bit multicore Linux. You can also download for 32-bit.

$ wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz

Installing IQ-TREE

Now extract the downloaded file.

$ tar xvzf iqtree-1.6.12-Linux.tar.gz

A new directory will be created namely, ‘iqtree-1.6.12-Linux‘. Move inside this directory and then to the bin directory.

$ cd iqtree-1.6.12-Linux/bin/

Here you will find an executable file namely, iqtree. Move or copy this file to the /usr/bin/ directory so that you can execute it from anywhere you want.

$ sudo cp iqtree /usr/bin/

Now IQ-TREE can be easily run by typing $ iqtree in the terminal.


References

  1. B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear(2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 37:1530-1534.

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

Software

How to execute matlab from terminal in Ubuntu (Linux)?

Published

on

How to execute matlab from terminal in Ubuntu (Linux)?

While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.

(more…)

Continue Reading

Software

How to install Kpax on Ubuntu (Linux)?

Published

on

How to install Kpax on Ubuntu (Linux)?

Kpax is a bioinformatics program to search and align protein structures [1]. It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux). (more…)

Continue Reading

Secondary structure

How to run do_dssp command (mkdssp) in Gromacs 2022?

Published

on

How to run do_dssp command in Gromacs 2022?

In the latest version of GROMACS (2022) [1], there are some issues regarding the gmx do_dssp command. Apparently, this command either does not run displaying a fatal error, or if it runs then it does not read any frame from MD simulation files. In this article, we are going to run the same command for GROMACS 2022. (more…)

Continue Reading

LATEST ISSUE

ADVERT