Available Software
Open source software packages will be installed as requested. Commercial packages require a discussion about licensing.
For select software packages (Freesurfer and FSL) we maintain local mailing lists. These can be useful for staying informed of software updates, or to discuss problems running the software on our cluster.
List of Software Packages
AFNI
Amber
ANNOVAR
ANTs
APBS
ART
ATAC-Seq
ATSAS
Augustus
AutoDock
AutoDock Vina
Bamtools
BayesTraits
BCFtools
Bcl2fastq
BEAST2
Bedtools2
Bowtie
Bowtie2
BWA
Cas-OFFinder
CASToR
CCP4
Cell Ranger
Censor
cisTEM
ClustalW
CMTK
Connectome Workbench
Coot
Critic2
CUDA
Cufflinks
dcm2niix
DTI-TK
EDGE-pro
Elastix
Espresso
FastQC
FASTX Toolkit
FreeSurfer
FSL
GATE
GATK
Gaussian
GCTA
Geant4
GEMMA
GeneTorrent
Graphviz
Gromacs
HISAT/HISAT2
HOMER
HTSlib
IMPUTE2
Infomap
Intel Compilers
JAGS
Java
jspr
Julia
kentUtils
LAMMPS
MATLAB
MethPipe
MGLtools
Mobster
Mothur
MRIcron
MuSTEM
NAMD
NCBI BLAST
.NET
NovoAlign
Octave
OpenCV
OpenEye
OpenFOAM
PALM
PANDAseq
PARalyzer
PEAR
Perl
PGI Compilers
PHENIX
PHP
Picard
Pigz
Pindel
PLINK
PORT
Python
QTLtools
Quantas
R
RazerS 3
RevBayes
RELION
RSEM
Rosetta
Sailfish
Samtools
SHAPEIT
SIMPSON
Singularity
SMRT Analysis
SNPTEST
SOLAR
SPM
SQL
SRA Toolkit
Stacks
STAR
Stata
STEMsalabim
STIR
StringTie
Tensorflow
Tinker
TM-score
Tophat
TORTOISE
Trim Galore!
USEARCH
VASP
VCFtools
Velvet