| [HTSlib](http://www.htslib.org/) | A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix |
| [HTSlib](http://www.htslib.org/) | A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix |
| [picard](http://sourceforge.net/projects/picard) | A set of tools (in Java) for working with next generation sequencing data in the BAM format. |
| [picard](http://sourceforge.net/projects/picard) | A set of tools (in Java) for working with next generation sequencing data in the BAM format. |
| [PLUMED](http://www.plumed-code.org) | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. |
| [PLUMED](http://www.plumed-code.org) | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. |
| Qualimap | Old module, description not available. |
| [RELION](http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page) | RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). |
| [RELION](http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page) | RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). |
| [Rosetta](https://www.rosettacommons.org) | Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. |
| [Rosetta](https://www.rosettacommons.org) | Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. |
| [SAMtools](http://www.htslib.org/) | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
| [SAMtools](http://www.htslib.org/) | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
