[Tutorial] Installing Rosetta 3.21 on Ubuntu
Rosetta is a bioinformatics software for modeling and protein structure analysis [1]. In this article, we are going to install this software on Ubuntu.
Installing PatchDock on Ubuntu (Linux)
PatchDock is a docking algorithm that is based on the shape complementarity principle [1,2]. It performs molecular docking of any two types of molecules including proteins, DNA, drugs, and peptides. In this article, we are going to install PatchDock on Ubuntu (Linux).
Easy installation of some alignment software on Ubuntu (Linux) 18.04 & 20.04
There are commonly used alignment programs such as muscle, blast, clustalx, and so on, that can be easily installed from the repository. In this article, we are going to install such software on Ubuntu 18.04 & 20.04.
Installing CDK (Chemistry Development Kit) on Ubuntu (Linux)
CDK stands for chemistry development kit [1]. This is an open source kit for cheminformatics consisting of modular JAVA libraries. In this article, we will install CDK on Ubuntu.
Installing Anaconda3 on Ubuntu (Linux)
Anaconda is an open-source toolkit that is useful in programming and machine learning using Python/R [1]. In this article, we are going to install Anaconda3 on Ubuntu (Linux).
Installing Pycharm on Ubuntu (Linux)
Pycharm [1] is an integrated development environment (IDE) for developers. It combines Python developer tools and provides an easy graphical user interface. In this article, we are going to install Pycharm on Ubuntu.
Installing RDPTools on Ubuntu (Linux)
RDP provides analysis tools called RDPTools. These tools are used to high-throughput sequencing data including single-strand, and paired-end reads [1]. In this article, we are going to install RDPTools on Ubuntu (Linux).
Tutorial: Basic Bioinformatics Software Installation on Ubuntu (Linux)
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.
Installing SAMtools on Ubuntu
SAMtools is a software package for high-throughput sequencing data analysis [1]. It consists of three separate packages: SAMtools, BCFtools, and HTSlib. We are going to install SAMtools only on Ubuntu. For the installation tutorial of BCFtools, click here.
Installing PANDAseq on Ubuntu
PANDAseq is a bioinformatics tool that aligns paired-ends of Illumina sequences [1]. In this article, we are going to install PANDAseq on Ubuntu.
Installing TopHat2 on Ubuntu
TopHat is one of the most widely used tools for RNA-seq reads to map splice junction [1]. It uses Bowtie to align mammalian genomes. The older versions of TopHat require the separate installation of SAMTools. But the versions 2.0 onwards come with an inbuilt stable SAMTools package. In this article, we will install TopHat2.1.1. on […]
Installing Bismark on Ubuntu
Bismark is a bioinformatics tool to map bisulfite treated sequencing reads to a genome [1]. It also determines cytosine methylation sites. In this article, we will install Bismark on Ubuntu.
How to install ClustalW2 on Ubuntu?
Clustal packages [1,2] are quite useful in multiple sequence alignments. Especially, when you need specific outputs from the command-line. In this article, we will install CustalW2 command-line tool on Ubuntu.
How to install Cortex on Ubuntu?
Cortex is a user-friendly framework for genome analysis [1]. It acquires less memory and is quite efficient in performance. It’s installation involves various steps. In this article, we will install Cortex on Ubuntu.
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.
Installing HMMER package on Ubuntu
HMMER tool is used for searching sequence homologs using profile hidden Markov Models (HMMs) [1]. It is also one of the most widely used alignment tools. In this article, we will install the latest HMMER package on Ubuntu.
Installing Cytoscape on Ubuntu
Cytoscape is a software for the easy visualization of complex networks [1-3]. In this article, we will install Cytoscape on Ubuntu.
Method-1: Installing GROMACS on Ubuntu with CUDA GPU Support
GROMACS [1] is one of the most popular software in bioinformatics for molecular dynamic (MD) studies of macromolecules. We have provided different tutorials regarding MD simulation using GROMACS including its installation on Ubuntu. In this article, we will install GROMACS with GPU acceleration.
Installing GROMOS96 on Ubuntu
GROMOS96 is a well-known software package used for biomolecular simulations [1]. It can be used for the molecular dynamics simulation of protein, peptide, and protein-ligand complex as well. In this article, we will install GROMOS96 on Ubuntu.
Installing MGLTools2 package (ADFR/AGFR/AutoSite) on Ubuntu
MGLTools2 package comes with three different tools for docking: ADFR, AGFR, and AutoSite [1-3]. In this article, we will install this package on Ubuntu.