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## Bio
| Module | Description |
| ------ | ----------- |
| [AlphaFold](https://github.com/sokrypton/alphafold) | AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known. This package of AlphaFold contains patches for ColabFold. |
| [Biopython](https://www.biopython.org) | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. |
| [BLAST](http://blast.ncbi.nlm.nih.gov/) | Basic Local Alignment Search Tool, or BLAST, is an algorithm for local_comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. |
| [BWA](http://bio-bwa.sourceforge.net/) | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. |
| [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. |
| [GATK](https://www.broadinstitute.org/gatk/) | The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. |
| [GROMACS](https://www.gromacs.org) | GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI builds. It also contains the gmxapi extension for the single precision MPI build. |
| [HH-suite](https://github.com/soedinglab/hh-suite) | The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). |
| [HMMER](http://hmmer.org/) | HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. |
| [Kalign](https://github.com/TimoLassmann/kalign) | Kalign is a fast multiple sequence alignment program for biological sequences. |
| [OpenMM](https://openmm.org) | OpenMM is a toolkit for molecular simulation. |
| [picard](https://broadinstitute.github.io/picard/) | A set of tools (in Java) for working with next generation sequencing data in the BAM format. |
| [Salmon](https://github.com/COMBINE-lab/salmon) | Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. |
| [snpEff](https://pcingola.github.io/SnpEff/) | SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). |
## Cae
| Module | Description |
| ------ | ----------- |
| [DualSPHysics](https://dual.sphysics.org/) | DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. The code is developed to study free-surface flow phenomena where Eulerian methods can be difficult to apply, such as waves or impact of dam-breaks on off-shore structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal with real-life engineering problems. |
| [OpenFOAM](https://www.openfoam.org/) | OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. |
## Chem
| Module | Description |
| ------ | ----------- |
| [ABINIT](https://www.abinit.org/) | ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. |
| [Amber](http://ambermd.org/amber.html) | Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. |
| [ASE](https://wiki.fysik.dtu.dk/ase) | ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations in C of functions in ASE. ASE uses it automatically when installed. |
| [BEEF](http://suncat.stanford.edu/facility/software/functional) | BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149. |
| [CheMPS2](https://github.com/SebWouters/CheMPS2) | CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. |
| [CoordgenLibs](https://github.com/schrodinger/coordgenlibs) | Schrodinger-developed 2D Coordinate Generation |
| [CP2K](https://www.cp2k.org/) | CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. |
| [DFT-D4](https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4) | Generally Applicable Atomic-Charge Dependent London Dispersion Correction. |
| [dftd3-lib](https://github.com/dftbplus/dftd3-lib) | This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules. |
| [GPAW](https://wiki.fysik.dtu.dk/gpaw/) | GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions. |
| [GPAW-setups](https://wiki.fysik.dtu.dk/gpaw/) | PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed. |
| [libcint](https://github.com/sunqm/libcint) | libcint is an open source library for analytical Gaussian integrals. |
| [libGridXC](https://launchpad.net/libgridxc) | A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems. It is based on SiestaXC. |
| [Libint](https://github.com/evaleev/libint) | Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. |
| [libxc](https://www.tddft.org/programs/libxc) | Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. |
| [Molden](http://www.cmbi.ru.nl/molden/) | Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac |
| [Molpro](https://www.molpro.net) | Molpro is a local_complete system of ab initio programs for molecular electronic structure calculations. |