MSI Software

Guidelines and Software Usage Protocol

MSI offers many software packages (listed below) for use by researchers in various fields of research. The MSI Software library below includes descriptions of software packages including many usage examples. 

To access software on Linux systems, please use the module command to load the software into your environment. If you try to run a certain program and get “command not found,” it may be because you need to load the module first. To use the software at MSI, you must first connect to a compute cluster, where you can then load modules and run the software.

Some software titles require a different login than your MSI user account. Please contact the Help Desk if the software you wish to use is password-protected. Depending on licensing, if the software is only available on select MSI machines, additional machines can be requested by contacting the Help Desk.

Software calendars and purchase requests

Title Last Updated On Support Level Software Access Level External Link Software categories
breakdancer 29/08/2023 Secondary Support Open Access Genetics
breseq 14/11/2023 Secondary Support Open Access Genetics
busco 28/11/2023 Primary Support Open Access Genetics
bwa 29/08/2023 Primary Support Open Access Genetics
bzip2 16/05/2024 Secondary Support Open Access Libraries
caffe 29/08/2023 Secondary Support Open Access Data Mining
cambridge-structural-database 29/08/2023 Secondary Support Open Access Molecular Modeling and Simulation | Spectroscopy | Database
cap3-contig-assembly-program 29/08/2023 Secondary Support Open Access Genetics
ccp4 29/08/2023 Secondary Support Open Access Structural Biology | Spectroscopy
cd-hit 29/08/2023 Secondary Support Open Access Genetics | Proteomics
cdo 29/08/2023 Secondary Support Open Access Geoscience | Libraries
ceas 29/08/2023 Secondary Support Open Access Genetics
celera-assembler 29/08/2023 Secondary Support Open Access Genetics
cesm 29/08/2023 Secondary Support Open Access Geoscience
cfitsio 29/08/2023 Secondary Support Open Access Geoscience | Libraries | Image Processing
cgal 14/11/2023 Secondary Support Open Access Libraries | Computational Geometry
cghub 29/08/2023 Secondary Support Open Access Genetics
charmm 29/08/2023 Secondary Support RESTRICTED - Contact Helpdesk Drug Discovery | Structural Biology | Electronic Structure | Molecular Modeling and Simulation | Spectroscopy
chenomx-nmr-suite 29/08/2023 Deprecated Open Access Biostatistics | Spectroscopy | Synthesis and Design
chimera 22/04/2024 Secondary Support Open Access Molecular Modeling and Simulation | Data Visualization
circos 29/08/2023 Secondary Support Open Access Data Visualization
clara-parabricks Secondary Support Open Access Genetics
clustalo 29/08/2023 Secondary Support Open Access Genetics
clustalx 29/08/2023 Secondary Support Open Access Genetics
cmake 12/06/2024 Primary Support Open Access Build Tools
cns 29/08/2023 Secondary Support Open Access Structural Biology
comsol 18/02/2025 Primary Support Limited Licenses Structural Engineering
conda 29/08/2023 Secondary Support Open Access Programming Languages | Libraries
connectome-workbench 15/04/2025 Secondary Support Open Access Biomedical Imaging
consed 29/08/2023 Secondary Support Open Access Genetics
coot 24/04/2024 Secondary Support Open Access Molecular Modeling and Simulation | Libraries
cp2k 03/12/2024 Primary Support Open Access Molecular Modeling and Simulation
cryosparc 15/04/2025 Secondary Support Open Access Drug Discovery | Life Sciences | Structural Biology
crystal 29/08/2023 Secondary Support Open Access Electronic Structure
cuda 14/11/2023 Primary Support Open Access Numerical Libraries | Optimization | Debugging and Performance
cuda-sdk 29/08/2023 Secondary Support Open Access Libraries
cudnn 08/12/2023 Secondary Support Open Access Libraries
cufflinks 29/08/2023 Secondary Support Open Access Genetics
curl 07/05/2024 Secondary Support Open Access Utilities
cutadapt 04/03/2025 Primary Support Open Access Genetics
cutesv 29/08/2023 Secondary Support Open Access Biostatistics | Genetics
cytoscape 29/08/2023 Secondary Support Open Access Pathway Analysis
defuse 28/11/2023 Secondary Support Open Access Genetics
desmond 29/08/2023 Secondary Support Open Access Drug Discovery | Structural Biology | Molecular Modeling and Simulation
diamond 14/11/2023 Secondary Support Open Access Genetics
discovery-studio 14/08/2024 Secondary Support Open Access Drug Discovery | Structural Biology | Electronic Structure | Molecular Modeling and Simulation
dlcpar 29/08/2023 Secondary Support Open Access Genetics
dock 29/08/2023 Secondary Support Open Access Drug Discovery | Molecular Modeling and Simulation | Synthesis and Design
duplicity 29/08/2023 Secondary Support Open Access Utilities
ea-utils 29/08/2023 Secondary Support Open Access Genetics