Software

A collection of published articles on different bioinformatics software.

Installing PyMol on Ubuntu

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PyMol is a molecular visualization software that is freely available for education-use-only [1]. PyMol provides an interface for the visualization of small and macromolecules. Besides, it provides various other functionalities including format export options such as PDB and poses import and export. It is also most widely used in analyzing the docking output obtained from other software such as Autodock Vina. We have previously provided tutorials on docking result analysis using Pymol. In this article, we will install Pymol on Ubuntu. Keep Reading

Homology search against a local dataset using NCBI-BLAST+ command-line tool

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NCBI-BLAST+ [1] command-line tool offers multiple functions to be performed on a large dataset of sequences. Previously, we have shown how to blast against a local dataset of sequences. This article will explain the search of homologous sequences for a query sequence against a local database of sequences and how to obtain the top 100 hits out of the searched results. Keep Reading

How to use Clustal Omega and MUSCLE command-line tools for multiple sequence alignment?

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Clustal Omega [1,2] and MUSCLE are bioinformatics tools that are used for multiple sequence alignment (MSA). In one of our previous articles, we explained the usage of the ClustalW2 command-line tool for MSA and phylogenetic tree construction. In this article, we will use Clustal Omega and MUSCLE for MSA exploring other arguments that facilitate different output formats. Keep Reading

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