Software Library
This inventory includes major software packages available on our compute systems. If you would like us to install a package not listed here, please let us know.
Can't find what you're looking for?
We are in the process of migrating all documentation to a new website. Point your browser to https://docs.rcc.fsu.edu and try your search there.
Available Software
ABINIT | 9.4.1 | Materials Modeling and Electronic Structure Calculations |
ADF | 2016.101 | Amsterdam Density Functional |
atsas | 3.0.3 | A program suite for small-angle scattering data analysis from biological macromolecules |
Charmm | 41 | A Computational Chemistry program for Molecular Modeling and Simulation |
Chimera | 1.8.1 | Molecular modeling system |
Crystal17 | Crystal17/1.0.2 | Software computing electronic wave function and properties of periodic systems |
Desmond | 3.4.0.2 | Simulation Software for Molecular Dynamics |
FPLO | 22.00-62 | The FPLO® package is a full-potential local-orbital code to solve the Kohn-Sham equations on a regular lattice or with free boundary conditions (finite systems) |
Gaussian | v16 | An application that provides state-of-the-art capabilities for electronic structure modeling |
GROMACS | 2021.2 | GROMACS is a versatile package to perform molecular dynamics |
GULP | 6.0 | Program for performing a variety of types of simulations on materials |
LAMMPS | 20201029 | Large-scale Atomic/Molecular Massively Parallel Simulator |
libxc | 4.3.0 | A DFT Exchange and Correlation Functionals Library |
moltemplate | 2.1.2 | A general text-based molecule builder for LAMMPS. |
NAMD | 2.14 | A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. |
nbo6 | 6.0 | The Natural Bond Orbital (NBO) program NBO 6.0 is a discovery tool for chemical insights from complex wavefunctions. |
NWChem | 7.0.2 | Application for high performance computational chemistry |
ORCA | 5.0.1; 4.1.2 | ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties |
P4VASP | 0.3.30 | An Open-Source Visualization Tool for VASP |
PyMOL | 2.5.0 | A molecular visualization system on an open-source Python foundation |
python-ase | 3.19.1 | ASE is an Atomistic Simulation Environment written in Python |
Quantum ESPRESSO | 6.5 | Nanoscale electronic-structure calculations and materials modeling |
VASP | 5.4.1;5.4.4 | The Vienna Ab initio Simulation Package is a computer program for atomic scale materials modelling. |
wannier90 | 3.0.0 | A tool for obtaining maximally-localised Wannier functions |
ABySS | 2.1.5 | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler |
ANGSD | 0.935 | ANGSD is a software for analyzing next generation sequencing data. |
ANTs | 2.3.5 | ANTs (Advanced Normalization Tools) is a program designed to do feature extraction on complex datasets with particular focus on images like MRI |
bcl2fastq | 2.20.0.422 | A Program to Convert BCL Data to FASTQ Format |
Beagle | 2.1 | Beagle is a High-Performance Bayesian and Maximum Likelihood Bioinformatics Library |
BEAST | 1.10.4 | BEAST is a Bayesian Analysis program for Building and Analyzing Phylogenetic Trees |
BEST | 3.1.2 | BEST is a Phylogenetics Program design to estimate Phylogenetic Trees |
Biopython | 1.79 | Python library for computational molecular biology. |
BLAT | 34 | A Low-Memory Footprint Genetic Sequence Alignment Tool |
Bowtie | 1.0.1 | Bowtie is an ultrafast, memory-efficient short read aligner |
Bowtie2 | 2.4.1. | Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences |
BWA | 0.7.17 | Software package for mapping low-divergent sequences |
Clustal W | 2.1 | A Program for Alignment of Multiple Genetic or Protein Sequences |
Clustal X | 2.1 | A Program for Alignment of Multiple Genetic or Protein Sequences (GUI Version of Clustal W) |
Cufflinks | 2.1.1 | Transcript assembly, differential expression, and differential regulation for RNA Sequencing |
DeepLabCut | User-Installed | A powerful Python package for animal pose estimation |
DSuite | 1.0.0 | A fast D-Statistics computation program |
ELPH | 0.1.5 | Motif Finding by Gibbs Sampling in DNA and Protein Sequences |
FASTA | 36.3.8e | Searching Biological Sequence Data for Regions of Similarity |
FASTQC | 0.11.8 | A quality control tool for high throughput sequence data. |
FreeSurfer | 7.1.1, 6.0.0 | FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. |
gemBS-rs | 4.0.0 | gemBS-rs is a rewrite of the gemBS pipeline using Rust. gemBS itself is a powerful high-throughput pipeline for DNA Methylation sequencing analysis. |
Glimmer | 3.02b | An Interpolated Markov Model Algorithm for Gene Finding in Microbial Genomes |
HTSeq | 0.13.5 | A Python Package for Analysis of High-Throughput Genetic Sequence Data |
MAFFT | 7.407 | A Program for Aligning Multiple Sets of Genetic Sequence Data |
Mauve | 2.4.0 | Aligning Multiple Genome Sequences with Large-Scale Evolutionary Events |
Migrate-n | 3.6.11, 4.4.0 | Estimates effective population sizes and past migration rates |
MrBayes | 3.2.1 | A Bayesian MCMC Program for Inferring Phylogenetic Models |
MUMmer | 3.23 | An Ultra-Fast Alignment Program for Genomic and Protein Sequence Data |
NiftyReg | 1.3.9 | An MRI Image Registration Tool |
RELION | 3.1.3 | RELION is a powerful biomacromolecular structure determination package for CryoEM applications. |
RNA-STAR | 2.4.1d | Ultrafast universal RNA sequencing aligner |
Samtools | 1.13 | Flexible generic format for storing nucleotide sequence alignments |
STAR | 2.5.3a | A Program for Ultrafast RNA-seq Sequence Alignments |
TopHat | 2.1.1 | A spliced read mapper for RNA Sequencing |
Trimmomatic | 0.36 | A flexible read trimming tool for Illumina NGS data |
VMD | 1.9.1 | VMD (Visual Molecular Dynamics) - Interactive Molecular Visualization and Analysis Software |
Agisoft Metashape | 2.0.1 | A stand-alone software product that performs photogrammetric processing of digital images and generates 3D spatial data to be used in GIS applications, cultural heritage documentation, and visual effects production as well as for indirect measurements of objects of various scales |
Apache Spark | 2.2.1 | A cluster computing framework for large-scale data processing |
Autoconf | 2.69 | GNU Autoconf is a package to automate the production of software configuration shell scripts |
bbFTP-client | 3.2.1 | The client program for bbFTP, which is designed for transfer of very large files |
Blender | 2.69 | Blender is a free and open source 3D animation suite |
CDO | 1.9.6 | CDO - Command Line Tools for Climate Model Data Analysis |
CMake | 3.13.3 | A Set of Tools to Simplify Building, Testing and Packaging Software |
CmdSTAN | 2.30.1 | CmdSTAN is an implementation of the STAN software package for Statistical modeling. It is a powerful source-to-source compiler which compiles STAN code to C++ from which a fast and optimized executable can be generated. |
DCRAW | 9.28.0 | A Linux Program for Decoding Raw Digital Image Files |
ffmpeg | 3.1.7 | Audio and Video Generation and Conversion Software |
FreeFem++ | 4.7 | Partial differential equation solver based on the finite element method |
Gephi | 0.9 | Gephi is an open-source visualization and exploration software for graphs and networks. Its interactive structure is beneficial for several different types of data analysis. |
Gerris | 1.3.2 | Solver of partial differential equations used in fluid flow. |
Git | 2.32.0.rc2 | Git - A Version Control System for Software Development |
Grace | 5.1.25 | A WYSIWYG 2D plotting tool for scientific graphing |
GrADS | 2.0.2 | GrADS - A Data Analysis and Display System for the Earth Sciences |
HADOOP | 1.2.1 (myhadoop-0.30) | Apache Hadoop is an open-source software framework for distributed storage and distributed processing of very large data sets on computer clusters built from commodity hardware. |
HDFView | 3.0.0 | A GUI Tool for Editing Files for the HDF4 and HDF5 Programs |
IPython | 7.16.1 | An Interactive Shell for Python with Jupyter Graphical Support |
JAGS | 4.2.0 | A Gibbs Sampler for Bayesian Hierarchical Models with MCMC |
Jupyter on OpenOnDemand | N/A | Detailed instructions on how to set up and use Jupyter on Open OnDemand |
Knight Lab Tools | Knight Lab Tools are a set of open-source tools developed by Northwestern University for data management, storytelling, and enhancing research through visualization. |
|
LibreOffice | 6.3.6.2 | LibreOffice is a powerful GUI application for word processing, spreadsheet calculation and database management |
Lmod | 7.8.9 | A Package to Dynamically Manipulate User Environments with Modules |
Model Coupling Toolkit (MCT) | 2.10.0 | Set of open-source software tools for creating coupled models |
Ncview | 2.1.8 | A Visualization Browser for netCDF Data |
NEdit | 5.7 | A graphical UNIX Text Editor |
OpenRefine | 3.6 | OpenRefine previously, known as Google Refine, is a common and important tool that helps us work with big messy data in many formats. It provides the ability to clean, format, or transform thousands of records at a time with a short learning curve for its basic functionalities. It will be particularly useful for those dealing with textual data in tables supporting over 15 languages and the following formats: |
parallel-kmeans | 1 | A Parallel Implementation of the K-Means Clustering Algorithm |
ParaView | 5.5.2 | ParaView is an open-source, multi-platform data analysis and visualization application |
ParMETIS | 4.0.3 | A Graph and Mesh Partitioning and Sparse Matrix Ordering Program |
pkg-config | 1.4.2 | A powerful and simple tool to find and compiler options for libraries. |
R (statistical computing) | 4.2.2 / Several Others | A popular, full featured, statistical computing package |
R Studio | R Studio is an integrated development environment R. It enables users to create programs using R language. |
|
SCOTCH | 6.0.6 | A Scientific Computing Library for Graph Partitioning and Mapping |
Singularity (Containers) | 3.8.1 | A powerful HPC Container Solution similar to and compatible with Docker |
Snort | 2.9.7.3 | A Powerful Open-Source Network Security Tool |
SPSS | 27 | SPSS is a powerful GUI statistics program built by IBM |
Spyder | Spyder is a scientific development environment designed for and written in Python. It features advanced tools and capabilities with the visualization of a scientific package. |
|
Stata | 13mp, 15, 16, 16mp | Stata is fully featured data analysis and statistical software |
tesseract | 5.2.0 | Tesseract is an open source optical character recognition (OCR) platform. OCR extracts text from images and documents without a text layer and outputs the document into a new searchable text file, PDF, or most other popular formats. Tesseract is highly customizable and can operate using most languages, including multilingual documents and vertical text. |
TotalView | 8.13.0, 2018.2.6, 2019.2.12, 2021.3.9 | A GUI-based parallel and serial debugging tool |
TurboMole | 7.4.1 | Program Package For Electronic Structure Calculations |
VisIt | 3.0.0 | A software package for visualizing scientific results |
WGRIB | 1.8.1.2c | A Program for Decoding and Working with GRIB Data Files |
ALPS | 2.1 | Algorithms and Libraries for Physics Simulations |
Armadillo C++ Library | 9.860.2 | A high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use |
ARPACK | 3.7.0 | A collection of Fortran77 subroutines designed to solve large scale eigenvalue problems |
BLAS | 3.2.1 | Linear Algebra Library |
Boost | 1.69.0 | Boost - A Powerful, Multipurpose library of C++ Tools |
DAQ | 2.0.6 | The Data Acquisition Library for the Snort IDS |
FFTW | 3.6.9 | C library to compute the discrete Fourier transforms |
FIAT | 1.6.0.dev0 | An Automatic Basis Function Tabulator for the Finite Element Package FEniCS |
fonttools | 3.8.0 | A Python library to Work With Text Font Files |
FSL | 6.0.5, 6.0.2 | FMRIB Software Library |
GSL | 1.6, 2.3, 2.6 | The GNU Scientific Library (GSL) is a powerful library of common numerical and scientific functions intended for use in C and C++ software. It serves as an important backend in many software packages. |
h5py | 2.8.0 | An API for the HDF5 Data Format for Python |
HDF4 | 4.2.15 | Tools and File Structures for Storing and Analyzing Scientific Data |
HDF5 | 1.10.4 | unique technology suite that makes possible the management of large and complex data |
Hypre | 2.18.2 | Library for solving large, sparse linear systems of equations on massively parallel computers |
LAPACK | 3.8.0 | Standard software library for linear algebra |
MPI for Python | 3.0.0 | An Implementation of MPI Bindings for Python |
MVAPICH2 | 2.3 | A Highly Scalable MPI Implementation for High-End Computer Systems |
NetCDF | 4.8.0(gcc/intel) 4.3.1(netcdf-cxx) 4.5.3 (fortran) | Libraries for representing scientific data |
OpenBLAS | 0.3.5 | A Highly Optimized Linear Algebra Library based on GotoBLAS |
OpenCV | 3.4.6 | A Powerful Library for Computer Vision Applications |
OpenMPI | 4.1.3, 4.1.0, 2.1.0 | An MPI Implementation for Parallel Computing |
PyTorch | 1.3.1 | A powerful machine learning library for Python |
ScaLAPACK | 2.0.2 | A High-Performance Linear Algebra Library |
SuperLU | 5.4.0, 5.2.1 | Library for the direct solution of large, sparse, nonsymmetric systems of linear equations. |
TensorFlow | 2.2.0 | A Powerful Deep Learning Library with GPU Support |
Anaconda | 2.7.15, 3.7.3, 3.8.3 | Python 2.7, 3.7 and 3.8 with 195 popular packages |
Chapel | 1.13.0 | A Modern Parallel Programming Language |
Clang | 6.0.0, 7.0.1 | A Front-End for LLVM-Based C Compilers |
CUDA | 11.1 | CUDA is a parallel computing platform and programming model for GPUs invented by NVIDIA. |
Cython | 0.29.12 | A Static Compiler for the Python and Cython Languages |
GNU Compilers | 8.3.1 | GNU C, C++, and Fortran Compilers |
GNU Octave | 5.2.0 | A high-level language, primarily intended for numerical computations |
Intel Compilers | 2021.2.0 | Intel C, C++, and Fortran Compilers |
Julia | 1.8.5 | A High-Performance Numerical Computing Environment and Language |
LLVM | 6.0.0 & 3.9.1 & 7.0.1 | A Toolkit for Building Compilers |
MATLAB | 2021b, 2020a, 2018b, 2017a, 2015b | A high-level language and interactive environment for numerical computation, visualization, and programming |
NASM | 2.15.03 | An Assembler for x86 Assembly Code |
NVHPC | 22.3 | NVIDIA's HPC Toolkit including CUDA Fortran, NVCC, NVC++ and other tools packaged with CUDA 11.6 |
Portland Group Compilers | 21.3.0 64-bit | PGI Compilers for C, C++, and Fortran |
Python | 3.10.4, 3.6.8, 2.7.17 | Interactive, object-oriented, extensible programming language |
yasm | 1.3.0 | A Modular Assembler code for x86 and AMD64 Assembly Code |