Computational biology focuses on creating algorithms and theoretical methods to solve biological problems. These algorithms then support the development of bioinformatics tools and software, which analyze biological data to generate insights. Here are commonly used bioinformatics software:
Commonly used bioinformatics software
| BLAST | Web and Standalone | Homepage |
| BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. It compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. | ||
Gromacs | OS: Linux, macOS, or Windows | Homepage |
| A free and open-source software suite for high-performance molecular dynamics and output analysis specifically designed for biochemical molecules like proteins, lipids, and nucleic acids. | ||
| AutoDock | OS: Linux, macOS, or Windows | Homepage |
| AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. | ||
| MEGA | OS: Linux, macOS, or Windows | Homepage |
| Molecular Evolutionary Genetics Analysis (MEGA) is a program for performing statistical analysis of molecular evolution and for constructing phylogenetic trees. | ||
| CLUSTAL | command line, web server versions | Homepage |
Clustal: Multiple Sequence Alignment of nucleic acid and protein sequences. Series comprises many tools, such as Clustal, ClustalW, ClustalV, ClustalΩ, ClustalX, and Clustal2. ClustalW is the most used MSA tool due to improved alignment, speed, and sensitivity than other available tools. Clustal Omega: The latest version of Clustal – fast and scalable, with greater accuracy due to the new HMM alignment engine; | ||
| PyMOL | OS: Linux, macOS, or Windows | Homepage |
PyMOL is a user-sponsored software for 3D visualization and analysis of biological macromolecules, maintained and distributed by Schrödinger. | ||
ChimeraX | OS: Windows | Homepage |
UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program. | ||
SPAdes | OS: Linux or MacOS | Homepage |
SPAdes is a versatile toolkit designed for the assembly and analysis of sequencing data. SPAdes is primarily developed for Illumina sequencing data but can be used for IonTorrent as well. Most of SPAdes pipelines support hybrid mode as supplementary data. | ||
FastQC | OS: Linux, Windows or MacOS | Homepage |
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. | ||
Trimmomatic | Command line (binary) | Homepage |
Trimmomatic: A flexible read trimming tool for Illumina NGS data, a more flexible and efficient preprocessing tool, which can correctly handle paired-end data. | ||
Cutadapt | macOS and Windows | Homepage |
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequences from your high-throughput sequencing reads. | ||
Celldesigner | OS: Linux, Windows or MacOS | Homepage |
CellDesigner is a free software for drawing and simulating gene-regulatory and biochemical networks using the Systems Biology Markup Language (SBML) and Systems Biology Workbench (SBW). | ||
MODELLER | OS: Linux, Windows or MacOS | Homepage |
MODELLER is a tool for creating three-dimensional models of proteins through homology or comparative modeling. It works by satisfying spatial restraints and offers additional features, such as de novo loop modeling, optimization of protein structures, multiple sequence or structure alignment, clustering, sequence database searching, and protein structure comparison. | ||
References
- Pathak, Rajesh Kumar, et al. “Introduction to Basics of Bioinformatics.” Elsevier eBooks, 2021, pp. 1–15. https://doi.org/10.1016/b978-0-323-89775-4.00006-7.
This information is provided for educational and research purposes only. There is no affiliation, endorsement, or partnership with the tool developers or associated institutions.
