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Tutorial: Basic Bioinformatics Software Installation on Ubuntu (Linux)

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Easy Installation of some Basic Bioinformatics Tools/Software

In this article, we are going to install some basic bioinformatics tools on Ubuntu from the repository. These tools include BLAST, HMMER, MUSCLE, MAFFT, several NGS analysis tools, and so on. This will be applicable to Ubuntu 16.04 or above.

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

Installing NCBI-BLAST+

$ sudo apt-get install -y ncbi-blast+

Installing HMMER

$ sudo apt-get install -y hmmer

Installing Jalview

$ sudo apt-get install -y jalview

Installing Abyss

$ sudo apt-get install -y abyss

Installing Jmol

$ sudo apt-get install -y jmol

Installing MAFFT

$ sudo apt-get install -y mafft

Installing MUSCLE

$ sudo apt-get install -y muscle

Installing CLUSTAL OMEGA

$ sudo apt-get install -y clustalo

Installing CLUSTALX

$ sudo apt-get install -y clustalx

Installing Mrbayes

$ sudo apt-get install -y mrbayes

Installing Njplot

$ sudo apt-get install -y njplot

Installing Phylip

$ sudo apt-get install -y phylip

Installing Phyml

$ sudo apt-get install -y phyml

Installing Pymol

$ sudo apt-get install -y pymol

Installing Rasmol

$ sudo apt-get install -y rasmol

Installing Readseq

$ sudo apt-get install -y readseq

Installing T-Coffee

$ sudo apt-get install -y t-coffee

Installing Avogadro

$ sudo apt-get install -y avogadro

Installing Bamtools

$ sudo apt-get install -y bamtools


These are some common bioinformatics tools that can be easily installed on Ubuntu 16.04 or above.

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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AlphaFill- New algorithm to fill ligands in AlphaFold models.

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AlphaFill- New algorithm to fill ligands in AlphaFold models.

AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,[2]. (more…)

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How to calculate binding pocket volume using PyVol plugin in PyMol?

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