17 Best Free and Open Source Linux Bioinformatics Tools

Bioinformatics has been defined in many different ways, but it is common ground to regard this discipline as the application of mathematics, computing and statistics to the analysis of biological information. The objective of bioinformatics is to enable the finding of new biological insights, and to create a broader, more critical view from which unifying principles in biology can be perceived.

Bioinformatics is very important in the field of human genome research. It has become crucial for large-scale measurement technologies such as DNA sequencing, microarrays, and metabolomics. The field of bioinformatics has been aided significantly by Linux-based hardware and software. There are a number of Linux distributions which offer an integrated bioinformatics workstation. The popular distribution Bio-Linux packages hundreds of bioinformatics programs spanning a number of different fields.

There’s a wide selection of Linux bioinformatics tools released under an open source license. This article identifies our favorite tools which are extremely useful for anyone interested in sequence analysis, molecular modelling, molecular dynamics, phylogenetic analysis and more. We hope this feature offers a useful resource for biologists.

Here’s our ratings chart showing our top picks. All the software featured is free and open source goodness.

Ratings chart for the best free and open source bioinformatics software

Let’s explore the 17 bioinformatics tools at hand. For each application we have compiled its own portal page, providing a screenshot of the software in action, a full description with an in-depth analysis of its features, together with links to relevant resources.

Bioinformatics Tools
BioconductorAnalysis and comprehension of high-throughput genomic data
BiopythonTools for biological computation written in Python
BioPerlPerl tools for computational molecular biology
IGVHigh-performance visualization genome browser tool
InterMineIntegrate biological data sources
GROMACSVersatile package to perform molecular dynamics
UGENESet of integrated bioinformatics software
BioJavaProvides Java tools for processing biological data
bedtoolsPowerful toolset for genome arithmetic
EMBOSSThe European Molecular Biology Open Software Suite
Clustal OmegaMultiple sequence alignment program
BLASTAlgorithm for comparing primary biological sequence information
Taverna WorkbenchFor designing and executing bioinformatics workflows
JalviewMultiple sequence alignment editing, visualisation and analysis
geWorkbenchSoftware platform for integrated genomic data analysis
BandageVisualising de novo assembly graphs
BioclipseRich-client platform chemistry and biology workbench
Best Free and Open Source SoftwareRead our complete collection of recommended free and open source software. Our curated compilation covers all categories of software.

The software collection forms part of our series of informative articles for Linux enthusiasts. There are hundreds of in-depth reviews, open source alternatives to proprietary software from large corporations like Google, Microsoft, Apple, Adobe, IBM, Cisco, Oracle, and Autodesk.

There are also fun things to try, hardware, free programming books and tutorials, and much more.
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