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 a chart showing our top picks.
So, let’s explore the 15 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.
|Bioconductor||Analysis and comprehension of high-throughput genomic data|
|Biopython||Tools for biological computation written in Python|
|BioPerl||Perl tools for computational molecular biology|
|InterMine||Integrate biological data sources|
|UGENE||Set of integrated bioinformatics software|
|IGV||High-performance visualization genome browser tool|
|BioJava||Provides Java tools for processing biological data|
|GROMACS||Versatile package to perform molecular dynamics|
|Taverna Workbench||For designing and executing bioinformatics workflows|
|EMBOSS||The European Molecular Biology Open Software Suite|
|Clustal Omega||Multiple sequence alignment program|
|BLAST||Algorithm for comparing primary biological sequence information|
|bedtools||Powerful toolset for genome arithmetic|
|geWorkbench||Software platform for integrated genomic data analysis|
|Bioclipse||Rich-client platform chemistry and biology workbench|
Read our complete collection of recommended free and open source software. The collection covers all categories of software.
The software collection forms part of our series of informative articles for Linux enthusiasts. There's tons 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.