Installing PatchDock on Ubuntu (Linux)

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).

Installing Anaconda3 on Ubuntu (Linux)

Installing anaconda on Ubuntu

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)

Installing pycharm on Ubuntu

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)

Installing RDPTools on Ubuntu

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).

Installing SAMtools on Ubuntu

Install 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

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

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

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?

Installing clustalw2 command-line tool 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 - genome analysis framework

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

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

Installing hmmer 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

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

Install gromacs with gpu acceleration

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

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.