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.
Visualization of running alignments of reads and contigs facilitates easy analysis and is useful in presenting assembly results. Several tools such as Artemis, BLAST Web, Circos,...
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...
A new utility is developed to convert variant calling format (VCF) files into HL7 FHIR format for the purpose of genomics electronic health records (EHR) integration....
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...
We use somatic variant callers to detect mutations in cancer samples by comparing sequencing data tumor and normal sample pairs. This is followed by some ad-hoc...
It is necessary to detect highly variable regions in envelopes of viruses as it allows the establishment of the viruses in the human body. A new...
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...
DIVERGE is a tool to detect functional divergence between member genes of a protein family based on (site-specific) shifted evolutionary rates after gene duplication or speciation...
A new webserver called DISTEVAL [1] is developed that evaluates the predicted protein distances. This web server evaluates the inter-residue distances and offers several other features...
As shown in previous articles, Pymol [1] has several functions. In this article, we will show how to look for disulfide in protein crystal structures using...
Pymol [1] has many functions that you keep finding on exploration. In this article, we will explain how to draw molecules in Pymol.
This video tutorial is in continuation of our previous tutorial.
A new command-line and web tool are developed for easy visualization of pedigree files. These files help to understand the complete family tree in case of...
Computational docking is an important technique in bioinformatics. The docking result interpretation and representation are important as well. There are various software available for docking result...
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....
genozip is a tool for lossless compression of large files including VCF, FASTQ, and SAM/BAM files [1]. In this article, we explain the usage of the...
Latest Comments