This is an old revision of the document!

Software for LifeScience Data Analyis

This page is currently under construction. It will hardly ever display a comprehensive/complete list:

  • We install many new tools upon request and it is hard to keep track documenting them all.
  • Software compiled / installed locally by projects is not supported by the HPC team and cannot be displayed here.

Links which are displayed in red, do not exist, yet. Any contribution or suggestion is welcome.

A note on limitations:

  • Benchmarks displayed on these pages are only benchmarks with respect to speed. The values are valid only for the given parameters and may greatly vary for deviating parameters or input. (You may indicate deviating experiences to us.)
  • We strive to improve the beauty and information content of this page. However, the conducted science is up to you as a user - whether or not a particular program invocation (the arguments supplied) actually make sense for your scientific question is up to you to decide.


News on software in bioinformatics and related stuff is distributed via a mailing list (low traffic). You can subscribe, too. You may also distribute and share information using this list.


Yes, please! Please get in touch with us, if you want to benchmark or contribute wrapper scripts. We created some repositories and would be delighted to add your name to the contributors. Also, contributions to this wiki (reports, suggestions, error notes) are welcome!

  • SeqAn – efficient applications of different areas *
  • BBMap – short read aligner + other tools *

Molecular Dynamics (MD) simulations are not confined to condensed matter physics, but of interest in the life sciences as well. They are, however, thematically attributed to physics. This page, therefore, merely indicates a link:

This wiki does not cover your topic / favourite software? Please let us know.

  1. We can install your software, which frequently is better than to install software yourself1), because:
    • we install software in an optimized fashion
    • if installed as a module, we made the commitment to support the software, if there are issues with the module, the batch system or I/O2)
  2. Writing wrapper scripts for otherwise non-performant applications can be cumbersome. We still encourage to approach us and ask us, before being stuck in a project.

Any contribution (a script, an idea, a reported issue, documentation, test data, own benchmark, etc.) is welcome! Particularly links labeled with “*” require attention3).

With the exception of abandonware, crappy software, scripts which can be installed with pip, cran, etc..
but, of course, not with respect to bugs within the software
Missing links wait to be filled with content - a re-structuring might also occur.
  • software/topical/lifescience.1536569453.txt.gz
  • Last modified: 2018/09/10 10:50
  • by meesters