| Exciting-code | | full-potential all-electron density-functional-theory (DFT) package based on the linearized augmented plane-wave (LAPW) method |
| FASTA | | package for aligning nucleotide or amino acid sequences |
| FASTX | | A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. |
| FEFF | | a real-space full multiple scattering (RSFMS) Green's function method |
| FFTW | | Freely available high performance library to perform fast Fourier transformations |
| FastQC | | Aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. |
| Fire | | commercial computational fluid dynamics package |
| Fluent | | commercial computational fluid dynamics package |
| FreeBayes | | Bayesian SNP and short indel caller from the Marth lab (who created Mosaik). |
| GAMESS | | ab initio quantum chemistry |
| GARLI | | Performs heuristic phylogenetic searches ... |
| GATK | | Structured software library for writing analysis tools for next-generation sequencing data. |
| GCTA | | A tool for Genome-wide Complex Trait Analysis |
| GENE | | plasma microturbulence code |
| GNU compiler collection | | compiler collection for a number of languages including C, C++ and Fortran |
| GPAW | | real-space DFT |
| GROMACS | | versatile package for molecular dynamics |
| Gaussian | | widely used quantum chemistry software |
| Gnuplot | | portable command-line driven graphing utility |
| Grace | | WYSIWYG tool to make two-dimensional plots of scientific data |
| Greens | | electronic structure codes based on the KKRASA Green's function technique |
| HMMER | | package for working with profile hidden Markov models (HMM) |
| Hkl2map | | is a graphical user-interface for macromolecular phasing |
| Inspector | | memory error and thread checker |
| Intel MPI | | MPI library |
| Intel compiler suite | | compilers for C, C++ and Fortran |
| Jaguar | | ab initio quantum mechanics |
| LAMMPS | | classical molecular dynamics code |
| MKL | | efficient mathematics library |
| MOLDEN | | display ab initio molecular densities |
| MPQC | | ab initio quantum chemistry |
| MSC Nastran | | Finite Element Analysis (FEA) solver |
| MUSIC | | C++ library for interprocess communication in large scale neuronal network simulations |
| MVAPICH2 | | MPI library |
| Mafft | | multiple sequence alignment program |
| Mathematica | | computational software for technical computing |
| Matlab | | programming language with extensive plotting and graphics functionalities |
| Meep | | finite-difference time-domain simulation software package |
| Molsim | | software for molecular dynamic, Monte Carlo, and Brownian dynamics simulation |
| MrBayes | | Bayesian estimation of phylogeny |
| Muscle | | fast, high-quality multiple sequence alignment |
| NAMD | | parallel molecular dynamics code |
| NCAR diagnostic packages | | climate model diagnostics |
| NCL | | analysis and visualization |
| NCO | | data analysis |
| NMRPipe | | NMR spectroscopy data analysis suite |
| NorESM | | global climate model |
| NumPy | | the fundamental package needed for scientific computing with Python |
| Octave | | numerical computation and visualisation language |
| Octopus | | time dependent density-functional theory code |
