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8 of the Best Free Linux Biology Tools

8 of the Best Free Linux Biology Tools

Biology is a natural science concerned with the study of living things, ranging from microscopic organisms up to the largest known animal, the blue whale. It is divided into many specialized fields including evolution, ecology, zoology, botany, genetics, microbiology and molecular biology. This science examines function, structure, origin, growth, evolution, distribution and taxonomy.

Biology is extremely relevant to our daily lives, as it helps us to understand how living things work, including the human body. Furthermore, the study of biology is crucial in the development of new food products, to protect the environmental quality of our world, and improving human health e.g. through the discovery of new medical treatments and tests for diseases.

Modern biology is founded on four main components: cell theory, evolution, gene theory, and homeostasis. Schools recognise the importance of biology to society, regarding it as one of the three most important branches of sciences, alongside physics and chemistry. We recently covered the best open source Linux software available for these disciplines in the following articles: Physics, Chemistry.

Biology is at the cutting edge of scientific research and development. In the past 40 years, biology has advanced enormously revealing a wealth of information about the millions of different organisms inhabitating our planet, including, of course, ourselves. Biology continues to grab the headlines with much excitement being generated in the fields of synthetic biology (combining science and engineering) and genomics (the study of the genomes of organisms).


There is a good range of open source biology software available for Linux. This article focuses on selecting our favorite tools which are extremely useful for biologists. We hope this feature offers a useful resource for biologists and students alike. With the diverse range of software, there should be something of interest here for all budding biologists.

So, let's explore the 8 biology 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 and reviews.

Biology Tools
EMBOSS The European Molecular Biology Open Software Suite
NAMD Parallel, object-oriented molecular dynamics
GROMACS Molecular dynamics simulator, with building and analysis tools
TreeView X Displays and prints phylogenetic trees
VMD Displays, animates, and analyzes large biomolecular systems
MUSCLE MUltiple Sequence Comparison by Log-Expectation
TREE-PUZZLE Reconstruction of phylogenetic trees by maximum likelihood
simuPOP Forward-time population genetics simulation environment

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Last Updated Wednesday, May 28 2014 @ 03:57 PM EDT


We have written a range of guides highlighting excellent free books for popular programming languages. Check out the following guides: C, C++, C#, Java, JavaScript, CoffeeScript, HTML, Python, Ruby, Perl, Haskell, PHP, Lisp, R, Prolog, Scala, Scheme, Forth, SQL, Node.js (new), Fortran (new), Erlang (new), Pascal (new), and Ada (new).


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