Available Software

The following software is documented for use at MSI.

Package Name	Support Level	Access Level
3dtests	Secondary Support	Open Access
abaqus	Secondary Support	Limited Licenses
abokia-blast	Secondary Support	Open Access
abyss	Secondary Support	Open Access
adam	Secondary Support	Open Access
adf	Secondary Support	Open Access
advisor	Secondary Support	Limited Licenses
afni	Secondary Support	Open Access
allpaths-lg	Secondary Support	Open Access
alphafold	Secondary Support	Open Access
amber	Secondary Support	Open Access
amira	Deprecated	Open Access
amos	Secondary Support	Open Access
ampl	Deprecated	Open Access
ams	Secondary Support	Open Access
anaconda	Secondary Support	Open Access
analyze	Secondary Support	Open Access
ansys-hfss	Secondary Support	Limited Licenses
ansys-maxwell-3d	Secondary Support	Limited Licenses
ansys	Secondary Support	Limited Licenses
antlr	Secondary Support	Open Access
ants	Secondary Support	Open Access
armadillo	Secondary Support	Open Access
artemis	Secondary Support	Open Access
aspera-client	Secondary Support	Open Access
atk	Secondary Support	Open Access
augustus	Secondary Support	Open Access
autoconf	Secondary Support	Open Access
autodock	Secondary Support	Open Access
automake	Secondary Support	Open Access
avizo	Secondary Support	Limited Licenses
bamtools	Primary Support	Open Access
bazel	Secondary Support	Open Access
bcftools	Primary Support	Open Access
beagle	Secondary Support	Open Access
beast	Secondary Support	Open Access
bedtools	Primary Support	Open Access
binutils	Primary Support	Open Access
bioinformatics	Secondary Support	Open Access
bioperl	Secondary Support	Open Access
biopython	Secondary Support	Open Access
blasr	Secondary Support	Open Access
blast-plus	Secondary Support	Open Access
blast	Secondary Support	Open Access
blat	Secondary Support	Open Access
boost	Primary Support	Open Access
bowtie2	Primary Support	Open Access
bowtie	Secondary Support	Open Access
braker1	Primary Support	Open Access
braker2	Secondary Support	Open Access
breakdancer	Secondary Support	Open Access
breseq	Secondary Support	Open Access
busco	Primary Support	Open Access
bwa	Primary Support	Open Access
bzip2	Secondary Support	Open Access
caffe	Secondary Support	Open Access
cambridge-structural-database	Secondary Support	Open Access
cap3-contig-assembly-program	Secondary Support	Open Access
ccp4	Secondary Support	Open Access
cd-hit	Secondary Support	Open Access
cdo	Secondary Support	Open Access
ceas	Secondary Support	Open Access
celera-assembler	Secondary Support	Open Access
cesm	Secondary Support	Open Access
cfitsio	Secondary Support	Open Access
cgal	Secondary Support	Open Access
cghub	Secondary Support	Open Access
charmm	Secondary Support	RESTRICTED - Contact Helpdesk
chenomx-nmr-suite	Deprecated	Open Access
chimera	Secondary Support	Open Access
circos	Secondary Support	Open Access
clara-parabricks	Secondary Support	Open Access
clustalo	Secondary Support	Open Access
clustalx	Secondary Support	Open Access
cmake	Primary Support	Open Access
cns	Secondary Support	Open Access
comsol	Primary Support	Limited Licenses
conda	Secondary Support	Open Access
connectome-workbench	Secondary Support	Open Access
consed	Secondary Support	Open Access
coot	Secondary Support	Open Access
cp2k	Primary Support	Open Access
cryosparc	Secondary Support	Open Access
crystal	Secondary Support	Open Access
cuda-sdk	Secondary Support	Open Access
cuda	Primary Support	Open Access
cudnn	Secondary Support	Open Access
cufflinks	Secondary Support	Open Access
curl	Secondary Support	Open Access
cutadapt	Primary Support	Open Access
cutesv	Secondary Support	Open Access
cytoscape	Secondary Support	Open Access
defuse	Secondary Support	Open Access
desmond	Secondary Support	Open Access
diamond	Secondary Support	Open Access
discovery-studio	Secondary Support	Open Access
dlcpar	Secondary Support	Open Access
dock	Secondary Support	Open Access
duplicity	Secondary Support	Open Access
ea-utils	Secondary Support	Open Access
eclipse	Secondary Support	Open Access
eggnog-mapper	Secondary Support	Open Access
eigen	Secondary Support	Open Access
emboss	Secondary Support	Open Access
ensight	Secondary Support	Open Access
enut	Secondary Support	Open Access
errut	Secondary Support	Open Access
esmf	Secondary Support	Open Access
espresso	Secondary Support	Open Access
evidencemodeler	Secondary Support	Open Access
exonerate	Secondary Support	Open Access
expat	Secondary Support	Open Access
falcon	Primary Support	Open Access
fasta36	Secondary Support	Open Access
fastme	Secondary Support	Open Access
fastqc	Primary Support	Open Access
fasttree	Primary Support	Open Access
fastx-toolkit	Secondary Support	Open Access
fca	Secondary Support	Open Access
febio	Secondary Support	Open Access
fenics	Secondary Support	Open Access
ferret	Secondary Support	Open Access
ffmpeg	Secondary Support	Open Access
fftw	Primary Support	Open Access
fgmp	Secondary Support	Open Access
fix	Secondary Support	Open Access
flann	Secondary Support	Open Access
flex	Secondary Support	Open Access
fraggenescan	Secondary Support	Open Access
freebayes	Primary Support	Open Access
freesurfer	Secondary Support	Open Access
freetype	Secondary Support	Open Access
fsl	Secondary Support	Open Access
fslview	Secondary Support	Open Access
funannotate	Secondary Support	Open Access
gamess	Secondary Support	Open Access
gatk-queue	Secondary Support	Open Access
gatk	Primary Support	Open Access
gaussian	Primary Support	RESTRICTED - Contact Helpdesk
gc	Secondary Support	Open Access
gdal	Secondary Support	Open Access
gdb	Secondary Support	Open Access
gdc-data-transfer-tool	Secondary Support	Open Access
genemark-et	Secondary Support	RESTRICTED - Contact Helpdesk
genetorrent-tools	Secondary Support	Open Access
genome-annotation-generator	Secondary Support	Open Access
genometools	Secondary Support	Open Access
geos	Secondary Support	Open Access
gettext	Secondary Support	Open Access
gflags	Secondary Support	Open Access
ghc	Secondary Support	Open Access
giflib	Secondary Support	Open Access
git	Secondary Support	Open Access
glew	Secondary Support	Open Access
glimmer	Secondary Support	Open Access
glimmerhmm	Secondary Support	Open Access
global-arrays	Secondary Support	Open Access
globus-command-line-interface	Secondary Support	Open Access
glog	Secondary Support	Open Access
gmap	Secondary Support	Open Access
gmp	Secondary Support	Open Access
gnu-compilers	Primary Support	Open Access
gnu-scientific-library	Secondary Support	Open Access
gnuplot	Secondary Support	Open Access
go	Secondary Support	Open Access
gopher-pipelines	Primary Support	Open Access
gpu-blast	Secondary Support	Open Access
grale-gamodules	Secondary Support	Open Access
grale	Secondary Support	Open Access
graleeditor	Secondary Support	Open Access
graleshell	Secondary Support	Open Access
graphpad-prism	Secondary Support	Limited Licenses
graphviz	Secondary Support	Open Access
gromacs	Primary Support	Open Access
guppy	Secondary Support	Open Access
gurobi	Secondary Support	RESTRICTED - Contact Helpdesk
gview	Secondary Support	Open Access
hadoop	Secondary Support	Open Access
haploview	Secondary Support	Open Access
hdf5-eos	Secondary Support	Open Access
hdf	Secondary Support	Open Access
hdfeos-netcdf	Secondary Support	Open Access
hisat2	Primary Support	Open Access
hmmer	Secondary Support	Open Access
hoard	Secondary Support	Open Access
hpctoolkit	Secondary Support	Open Access
hpmpi	Secondary Support	Open Access
htseq	Secondary Support	Open Access
htslib	Secondary Support	Open Access
huygens	Secondary Support	Open Access
hwloc	Secondary Support	Open Access
hyphy	Primary Support	Open Access
hypre	Secondary Support	Open Access
idl	Secondary Support	Open Access
igv	Secondary Support	Open Access
ilog	Secondary Support	Open Access
imagej	Secondary Support	Open Access
imaris	Secondary Support	Limited Licenses
inspector	Secondary Support	Open Access
integer-set-library	Secondary Support	Open Access
intel-compilers	Primary Support	Limited Licenses
intel-mpi	Primary Support	Limited Licenses
interproscan	Secondary Support	Open Access
ipa	Deprecated	Open Access
itac	Secondary Support	Limited Licenses
itk-snap	Secondary Support	Open Access
jacket	Secondary Support	Open Access
jags	Secondary Support	Open Access
java	Primary Support	Open Access
jellyfish	Secondary Support	Open Access
jemalloc	Secondary Support	Open Access
jets3t	Secondary Support	Open Access
jthread	Secondary Support	Open Access
kallisto	Secondary Support	Open Access
kent-genomics-tools	Secondary Support	Open Access
keras	Secondary Support	Open Access
lammps	Secondary Support	Open Access
last	Secondary Support	Open Access
lastz	Secondary Support	Open Access
leveldb	Secondary Support	Open Access
libcairo	Secondary Support	Open Access
libdrmaa	Secondary Support	Open Access
libedit	Secondary Support	Open Access
libgd	Secondary Support	Open Access
liblpsolve	Secondary Support	Open Access
liblzma	Secondary Support	Open Access
libmatheval	Secondary Support	Open Access
libsequence	Secondary Support	Open Access
libsvm	Secondary Support	Open Access
libtiff	Secondary Support	Open Access
libtool	Secondary Support	Open Access
libungif	Secondary Support	Open Access
libunistring	Secondary Support	Open Access
libxcb	Secondary Support	Open Access
libxz	Secondary Support	Open Access
llvm	Secondary Support	Open Access
lmdb	Secondary Support	Open Access
longranger	Secondary Support	Open Access
lumerical-fdtd	Secondary Support	RESTRICTED - Contact Helpdesk
lumerical_device	Secondary Support	Open Access
lumerical_interconnect	Secondary Support	Open Access
lumerical_modesolutions	Secondary Support	Open Access
lumpy	Secondary Support	Open Access
macs	Primary Support	Open Access
mafft	Secondary Support	Open Access
magma	Secondary Support	Open Access
maker	Secondary Support	Open Access
mamba	Secondary Support	Open Access
materials-studio	Secondary Support	RESTRICTED - Contact Helpdesk
mathematica	Secondary Support	RESTRICTED - Contact Helpdesk
matlab	Primary Support	Limited Licenses
maven	Secondary Support	Open Access
mcl	Secondary Support	Open Access
mega	Secondary Support	Open Access
megan	Secondary Support	Open Access
mercurial	Secondary Support	Open Access
metal	Secondary Support	Open Access
metamos	Secondary Support	Open Access
metaphlan2	Secondary Support	Open Access
metis	Secondary Support	Open Access
mimics	Secondary Support	Limited Licenses
minimap2	Secondary Support	Open Access
mira	Secondary Support	Open Access
mkl-and-cmkl	Secondary Support	Open Access
moe	Secondary Support	Open Access
mogal	Secondary Support	Open Access
molden	Secondary Support	Open Access
molekel	Secondary Support	Open Access
molpopgen	Secondary Support	Open Access
molpro	Secondary Support	Open Access
monolix	Secondary Support	Limited Licenses
mopac	Secondary Support	Open Access
mosaik	Secondary Support	Open Access
mothur	Secondary Support	Open Access
mpc	Secondary Support	Open Access
mpfr	Secondary Support	Open Access
mpiblast	Primary Support	Open Access
mpich	Secondary Support	Open Access
mrbayes	Secondary Support	Open Access
mricrogl	Secondary Support	Open Access
msff	Secondary Support	Open Access
msstats	Secondary Support	Open Access
mummer	Primary Support	Open Access
mumps	Secondary Support	Open Access
muscle	Secondary Support	Open Access
mvapich	Secondary Support	Open Access
mxm	Secondary Support	Open Access
namd	Primary Support	Open Access
nanocount	Secondary Support	Open Access
nanofilt	Secondary Support	Open Access
nanoplot	Secondary Support	Open Access
nanostat	Secondary Support	Open Access
nanosv	Secondary Support	Open Access
ncbi_toolkit	Primary Support	Open Access
nccl	Secondary Support	Open Access
ncdu	Secondary Support	Open Access
ncl	Secondary Support	Open Access
nco	Secondary Support	Open Access
ncview	Secondary Support	Open Access
nedit	Secondary Support	Open Access
netcdf	Secondary Support	Open Access
neuron	Secondary Support	Open Access
nonmem-0	Secondary Support	Limited Licenses
nseg	Secondary Support	Open Access
nvbio	Secondary Support	Open Access
nwchem	Secondary Support	Open Access
oases	Secondary Support	Open Access
octave	Secondary Support	Open Access
omega	Secondary Support	Open Access
openbabel	Secondary Support	Open Access
openbugs	Secondary Support	Open Access
opencl	Secondary Support	Open Access
opencv	Secondary Support	Open Access
openfoam	Secondary Support	Open Access
openmpi	Primary Support	Open Access
openstack-cli	Secondary Support	Open Access
orca	Secondary Support	Open Access
origin-lab	Secondary Support	Open Access
orthofinder	Secondary Support	Open Access
paml	Secondary Support	Open Access
pandaseq	Secondary Support	Open Access
papi	Secondary Support	Open Access
parallel	Primary Support	Open Access
paraview	Secondary Support	Open Access
parmetis	Secondary Support	Open Access
partek-genomics-suite	Deprecated	Limited Licenses
pasa	Secondary Support	Open Access
pcl	Secondary Support	Open Access
pcre	Secondary Support	Open Access
pear	Secondary Support	Open Access
perfsuite	Secondary Support	Open Access
perl	Secondary Support	Open Access
petsc	Secondary Support	Open Access
pgi-cdk	Primary Support	Open Access
phat	Secondary Support	Open Access
phenix	Secondary Support	Open Access
phobius	Secondary Support	Open Access
phrap	Secondary Support	Open Access
phred	Secondary Support	Open Access
phylip	Secondary Support	Open Access
phyml	Secondary Support	Open Access
picard-tools	Primary Support	Open Access
picrust2	Secondary Support	Open Access
pig	Secondary Support	Open Access
pilon	Primary Support	Open Access
plink	Secondary Support	Open Access
pmpi	Secondary Support	Open Access
pnetcdf	Secondary Support	Open Access
pomoxis	Secondary Support	Open Access
porechop	Secondary Support	Open Access
postgresql	Secondary Support	Open Access
postview	Secondary Support	Open Access
povray	Secondary Support	Open Access
primer3	Secondary Support	Open Access
prinseq	Secondary Support	Open Access
probabel	Secondary Support	Open Access
prodigal	Secondary Support	Open Access
proj	Secondary Support	Open Access
proteinortho	Secondary Support	Open Access
protobuf	Secondary Support	Open Access
psqlodbc	Secondary Support	Open Access
pymol	Secondary Support	Open Access
python2	Primary Support	Open Access
python3	Primary Support	Open Access
python	Primary Support	Open Access
qchem	Secondary Support	Open Access
qhull	Secondary Support	Open Access
qiime2	Secondary Support	Open Access
qiime	Secondary Support	Open Access
qt	Secondary Support	Open Access
quake	Secondary Support	Open Access
quast	Primary Support	Open Access
qwt	Secondary Support	Open Access
r-rich	Primary Support	Open Access
r	Primary Support	Open Access
racon	Secondary Support	Open Access
ragel	Secondary Support	Open Access
raxml	Primary Support	Open Access
rclone-browser	Secondary Support	Open Access
rclone	Secondary Support	Open Access
readline	Secondary Support	Open Access
recon	Secondary Support	Open Access
reframe-hpc	Secondary Support	Open Access
repeat-masker	Secondary Support	Open Access
repeatmodeler	Secondary Support	Open Access
repeatscout	Secondary Support	Open Access
rhothetapost	Secondary Support	Open Access
ribopicker	Secondary Support	Open Access
riss_util	Primary Support	Open Access
rmblast	Secondary Support	Open Access
rnammer	Secondary Support	RESTRICTED - Contact Helpdesk
roche454	Secondary Support	RESTRICTED - Contact Helpdesk
root	Secondary Support	Open Access
rosetta	Secondary Support	RESTRICTED - Contact Helpdesk
rsem	Secondary Support	Open Access
rstudio	Secondary Support	Open Access
ruby	Secondary Support	Open Access
sam-tools	Primary Support	Open Access
saoimage-ds9	Secondary Support	Open Access
sap	Secondary Support	Open Access
scalapack	Secondary Support	Open Access
scalasca	Secondary Support	Open Access
schrodinger	Primary Support	Limited Licenses
scons	Secondary Support	Open Access
sequtils	Secondary Support	Open Access
serut	Secondary Support	Open Access
sga	Secondary Support	Open Access
shellp	Secondary Support	Open Access
shelx	Secondary Support	Open Access
sicer	Secondary Support	Open Access
siesta	Secondary Support	Open Access
signalp	Secondary Support	RESTRICTED - Contact Helpdesk
slicer3d	Secondary Support	Open Access
snap	Secondary Support	Open Access
snappy	Secondary Support	Open Access
sniffles	Secondary Support	Open Access
soap	Secondary Support	Open Access
spades	Primary Support	Open Access
spark	Secondary Support	Open Access
sparsehash	Secondary Support	Open Access
speedseq	Secondary Support	Open Access
sprng	Secondary Support	Open Access
sra-toolkit	Secondary Support	Open Access
ssaha2	Secondary Support	Open Access
star	Primary Support	Open Access
stata	Secondary Support	RESTRICTED - Contact Helpdesk
structure	Secondary Support	Open Access
subversion	Secondary Support	Open Access
suitesparse	Secondary Support	Open Access
supermongo	Secondary Support	Open Access
swig	Secondary Support	Open Access
szip	Secondary Support	Open Access
t-coffee	Secondary Support	Open Access
tandem-genotypes	Secondary Support	Open Access
tbl2asn	Secondary Support	Open Access
tcl	Secondary Support	Open Access
tcltk	Secondary Support	Open Access
tecplot	Secondary Support	Open Access
tensorflow	Secondary Support	Open Access
texlive	Secondary Support	Open Access
textadept	Secondary Support	Open Access
tmhmm	Secondary Support	RESTRICTED - Contact Helpdesk
tmux	Secondary Support	Open Access
tophat	Secondary Support	Open Access
trackd	Secondary Support	Open Access
transdecoder	Secondary Support	Open Access
trf	Secondary Support	Open Access
trimal	Secondary Support	Open Access
trimmomatic	Primary Support	Open Access
trinity	Secondary Support	Open Access
trinotate	Primary Support	Open Access
tripos-sybyl	Secondary Support	Open Access
trnascan	Secondary Support	Open Access
turbomole	Secondary Support	Open Access
uclust	Secondary Support	Open Access
udunits	Secondary Support	Open Access
umgc	Secondary Support	Open Access
unafold	Secondary Support	Open Access
usearch	Secondary Support	RESTRICTED - Contact Helpdesk
valgrind	Secondary Support	Open Access
vasp	Primary Support	RESTRICTED - Contact Helpdesk
vcflib	Primary Support	Open Access
velvet	Secondary Support	Open Access
visual-studio	Secondary Support	Open Access
vlc	Secondary Support	Open Access
vmd	Secondary Support	Open Access
vsearch	Secondary Support	Open Access
vtk	Secondary Support	Open Access
vtune	Secondary Support	Open Access
wannier	Secondary Support	Open Access
weka	Secondary Support	Open Access
whirlgif	Secondary Support	Open Access
wrf	Secondary Support	Open Access
xerces	Secondary Support	Open Access
xqilla	Secondary Support	Open Access
xz-utils	Secondary Support	Open Access
zlib	Secondary Support	Open Access
zsh	Secondary Support	Open Access