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...
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...
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...
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...
PANDAseq is a bioinformatics tool that aligns paired-ends of Illumina sequences [1]. In this article, we are going to install PANDAseq on Ubuntu.
We have provided a tutorial on installing GROMACS [1] on Ubuntu with CUDA GPU support. The methods may vary depending on the requirements of your system....
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...
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...
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...
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...
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...
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....
Cytoscape is a software for the easy visualization of complex networks [1-3]. In this article, we will install Cytoscape on Ubuntu.
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...
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...
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.
BCFtools is a set of utilities that are used to manipulate variant call files (VCF) and binary call files (BCF). It can be used for both...
FragGeneScan is a bioinformatics software to find fragmented genes in short reads [1]. It predicts genes by combining sequence models and codon usages in a hidden...
Molecular dynamics (MD) simulation is considered amongst the important methods in bioinformatics. Installation of MD simulation software and execution of their commands is critical. It requires...
MEME suite is used to discover novel motifs in unaligned nucleotide and protein sequences [1,2]. In this article, we will learn how to install MEME on...