3D-Caffe, Caffe, Caffe2, libgpuarray, Mxnet, OpenCV, Root, Stxxl, TensorFlow, Torch

Abaqus, Ansys, AnsysEM, CGNS, Gmsh, Gurobi, LS-DYNA, LS-PrePost, Nastran, OpenFOAM, Yade

Abricate, Abyss, Abyss-mpi, AdapterRemoval, AfterQC, Aligngraph, AlleleSeq, Allpathslg, AmrPlusPlus, Annovar, Aragorn, armatus, Artemis, ArtificialFastqGenerator, Augustus, bam-readcount, Bambamc, Bamtools, bamUtil, barrnap, BASE, Basespace, BatMeth, BayesAss, Bbmap, BCFtools, Bcl2fastq, Beagle, Beast, BEDOPS, Bedtools, biobambam2, Biopieces, Bismark, Blasr, Blast, BLAST+, Blat, BlobTools, Bowtie, Bowtie2, bpp, Bracken, BRAKER1, BRAKER2, Brig, Busco, Bvatools, BWA, Canu, Cap3, Cd-Hit, Centrifuge, Chimera, Chimeraslayer, ChunkChromosome, Clonalframeml, Clustal Omega, Clustal W/X, Codonphyml, coevol, Cortex, Crest, Cufflinks, Cutadapt, Delly, DETONATE, Diamond, Drive5, Ea-Utils, EDirect, Emboss, EMMAX, EPA-ng, Epacts, EVidenceModeler, ExaBayes, EXCAVATOR2tool, exonerate, Falcon, Falcon-Unzip, Fastml, fastp, fastPHASE, FastQC, fastQValidator, Fasttree, Fastx, FImpute, Flash, fqgrep, fqtools, FRANz, freebayes, funannotate, FUSTr, gatb, Gatk, Gblocks, gcta, gem-tools, Gemma, GeneMark-ES, Genomemasker, GenomeTools, Gess, giremi, gmap, GraPhlAn, GraPhlAn, GRIDSS, Gubbins, Haddock, hapcut, Hapcut, Hapflow, haplotyper, Haploview, Hapsembler, Hh-Suite, HiC-bench, HiCUP, HISAT2, hlascan, Hmmer, Homer, hotspotter, HTSlib, I-Tasser, Idba, idp, Igvtools, IMPUTE2, Infernal, IQ-TREE, Is_Mapper, ITSx, Iva, Jaspa, Jellyfish, Juicer, Kalign, kallisto, Kat, kentutils, Kmc, Kraken, Kraken2, LAST, libmaus2, lighter, Lofreq, longranger, lordec, lumpy-sv, MACH, MaCH-Admix, MAFFT, Magic-BLAST, Maker, Manta, MARVEL, Mash, MATAM, Mauve, Medusa, Megacc, Megahit, megan, MELT, Meme, MetaPhlAn2, Metatissue, Methpipe, MethylDackel, Migrate-N, minced, Minimac2, Minimac4, Minimap2, Mira, Mirdeep2, MISTReSS, Mlst, Mothur, mpiBWA, Mrbayes, Mugsy, Mummer3, Mummer4, Mutect, Mykrobe-Predictor, NanoOk, Nanopolish, NCBI C++ Toolkit, Newick-Utils, Norgal, Nullarbor, oases, Paml, pandaseq, Pblat, Pear, PennCNV, pgdspider, phase, Pheniqs, PHYLIP, PhyloBayes, Phyml, Picard, Pilon, Pindel, Pipits, Platypus, PLINK, PneumoCaT, Prank, Preseq, Prinseq, Prodigal, Prokka, ProteinOrtho, PSIPRED, PSMC, Purge Haplotigs, Qiime, Qorts, Qualimap, Quast, QuickTree, Racon, Ragout, RAiSD, Ray, Rdpclassifier, Readseq, REAPR, Reddog, Repeatmasker, Repeatmodeler, RepeatScout, Rmats, Rnammer, Roary, Rosetta, RSEM, salmon, sam2bam, Sambamba, Samblaster, samclip, Samtools, scotti, selscan, seqOutBias, Seqtk, sff2fastq, Sga, SHAPEIT, Shorah, ShortStack, shovill, Sibelia, Signalp, SiLiX, SKESA, Smalt, SMRT, SMRTtools, SNAP, Snippy, snp-dists, SNP-sites, SnpEff, SNPhylo, SOAPdenovo2, SortMeRNA, Spades, SpeedSeq, Sratoolkit, STACKS, Stampy, Star, Strainseeker, Strelka, Stringtie, subread, Subread, Supernova, Surpi, Svtyper, Tabix, Tbl2Asn, Tophat, Tracer, Transdecoder, trimAl, Trimgalore, Trimmomatic, Trinity, Trinotate, tRNAscan-SE, UCSC Genome Browser, Usearch, UVP, Varscan, VaST, vcf2diploid, Vcftools, Velvet, VelvetOptimiser, ViennaRNA, Vmatch, Vsearch, WALT, Wgs, wgsim, XHMM, XP-EHH

afni, Amos, ANTs, ASHS, c3d, camino, Conn, dcm2niix, Dcmtk, DTI-TK, Fix, Freesurfer, Fsl, Gamos, Gate, MIPAV, MRtrix3, rtk

Ag, Aria2, Autoconf, Automake, bzip2, curl, Cyberduck, Gdc-Client, Gettext, gtextutils, jq, Libunistring, Lzma, M4, Mawk, Pandoc, pigz, RapidJSON, Readline, Snappy, Xdrfile

Anaconda, Anaconda2, Argtable2, Bazel, Binutils, Bison, Cmake, Dbus, Dbus-Glib, Doxygen, Expat, Flex, Fontconfig, Gdl, Gflags, Git, Glib, Graphviz, Guile, Icmake, Icu, Jupyter, Leveldb, Libcroco, Libcurl, Libffi, Libgc, Libmng, Libspatialite, Libspectre, Libtau, Libtiff, Libtool, Libxml2, Libxslt, Luabind, Luajit, Maven, Mercurial, Ncurses, Node, Pango, Pcre, Pcre2, Protobuf, Raxml, Raxmls, Scons, Slang, Sparsehash, Spatialite, Sphinx, Subversion, Swig, tre, Udunits, Vcflib, Xmlto, Yasm

Ann, Epimine, Gephi, Glog, Harfbuzz, libevent, Lmdb, Modeller, Mono, MTBseq, OpenSSL, Osrm, Readosm, SDL, SDL_image, tmux, yaml-cpp

Ant, GadgetViewer, Geant4, Tomographer, wcslib

Armadillo, Arpack-Ng, Atlas, Baps, Blas, Boost, Cblas, Cddlib, CGAL, Clhep, Eigen, Eigenvalue SoLvers for Petaflop-Applications (ELPA), FFTW, Geos, GHMM, Gmp, Gsl, GTS, Highwayhash, HYPRE, Lapack, Libmatheval, Libsodium, libspatialindex, Loki, Lsd, METIS, Mpc, Mpfr, Nettle, Nlopt, OpenBLAS, Qhull, Routino, ScaLAPACK, Scotch, SLEPc, Suitesparse

Biogeme, Go, Jags, Mcl, Netgen, Netlogo, Underworld 2

Cairo, cairomm, Circos, Ffmpeg, FreeGLUT, Freetype, Ghostscript, Gnuplot, Graphicsmagick, Idl, Imagej, Imagemagick, Imp, Jasper, libfreeimage, Libgd, Libjpeg, Libpng, libQGLViewer, MathGL, MayaVi, OpenJPEG, Paraview, Photoscan-Pro, Pixman, Plplot, Poppler, Povray, Pslib, Simple, Visit, Vmd, Vtk

CFITSIO, Freexl, GL2PS, HDF5, Hiredis, Intltool, Libelf, Ncview, NetCDF, Xz, Zlib

Cuda, Cuda2, Gperftools, Intel-MPI, Mpich, MVAPICH2, OpenMPI-gcc, OpenMPI-Intel, OpenMPI-PGI, Parallel, Spark, Tbb, Zeromq

Dlpoly, Exciting, gaussian, Gromacs, Gromacs-Plumed, Hoomd, Lammps, LIGGGHTS-PUBLIC, LIGGGHTS-with-bonds, Macs, Molpro, NAMD, ORCA, Plumed, Pymol, Qe, Siesta, XCrySDen

Ec2-Api-Tools

Armadillo, Arpack-Ng, Atlas, Baps, Blas, Boost, Cblas, Cddlib, CGAL, Clhep, Eigen, Eigenvalue SoLvers for Petaflop-Applications (ELPA), FFTW, Geos, GHMM, Gmp, Gsl, GTS, Highwayhash, HYPRE, Lapack, Libmatheval, Libsodium, libspatialindex, Loki, Lsd, METIS, Mpc, Mpfr, Nettle, Nlopt, OpenBLAS, Qhull, Routino, ScaLAPACK, Scotch, SLEPc, Suitesparse

emacs

FEniCS, HEALPix, Macaulay2, Mathematica, Matlab, Mcr, petsc, PHCpack, SAS, SUNDIALS

gcc, Intel, Java, NASM, Pgi

Gdal, Proj, Proj.4, Rgdal, VAPOR, Virtualpg

Gdb, Re2, Valgrind

gengetopt, Zstd

Julia, Lua, Nextflow, nim, Octave, Perl, Python, Qt, Qwt, R, Rstudio, Ruby, Scala, Tcl, Tk

MongoDB, MySQL, Pgsql, RocksDB, Sqlite

Multiresolution domain calling software for chromosome conformation capture interaction matricies.

2.2

module load armatus

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.

1.1-intel, 1.2, 1.3.1, 1.3.1-intel, 1.5, 1.5-intel, 1.6, 1.6-intel, 1.8, 1.9, 1.9-102

module load bcftools/xxx (where xxx represents the version number)

BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS

1.9

module load braker1

Cross-platform, open-source build system.

3.0.1, 3.4.0, 3.9.4, 3.11.4, 3.13.4

module load cmake/xxx (where xxx represents the version number)

CUDA is NVIDIA's parallel computing architecture.

6.0.37, 6.5.14-test, 6.5.14, 7.5.18, 8.0.44, 9.0.176, 9.1.85, 9.2.148, 10.0.130, 10.1.105

module load cuda/xxx (where xxx represents version number)

The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures.

v1.1.1

module load evidencemodeler

Funannotate is a pipeline for genome annotation (built specifically for fungi, but theoretically should work with other eukaryotes).

0.7.2, 1.2

module load funannotate/0.72 or module load funannotate/1.2

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data.

3.3.0, 3.4.0, 3.6.0, 3.7.0, 3.8.0, 3.8.1, 4.0.2.1, 4.0.8.1

module load gatk/xxx (where xxx represents version number)

Mining CRISPRs in Environmental Datasets

0.2.0, 0.3.3

module load minced/xxx (where xxx is the version)

OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.

2.3.1, 2.4.0, 3.0.1, 3.0.1-intel, 3.0.x, 4.0, 4.1, 4.1-intel, 5.0, v1612+, v1712, 6

OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.

The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.

7.0, 8.39, 8.41

module load pcre/xxx (where xxx is the version)

A set of tools (in Java) for working with next generation sequencing data in the BAM format.

1.119, 1.134, 2.1.1, 2.7.1, 2.18.4, 2.18.23

module load picard/xxx (where xxx represents version number)

Proteinortho is a tool to detect orthologous genes within different species.

v5.16

module load proteinortho

RAiSD (Raised Accuracy in Sweep Detection) is a stand-alone software implementation of the _ μ statistic for selective sweep detection.

1.7

modue load raisd

SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering.

2.1b, 3.0.3

module load shortstack/2.1bsortmerna/xxx (where xxx is the version)

Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source.

1.1.5, 2.1.1

module load supernova/xxx (where xxx is the version)

A tool for automated alignment trimming in large-scale phylogenetic analyses.

1.4.1

module load trimal

tRNAscan-SE: An improved tool for transfer RNA detection.

1.3.1

module load tRNAscan/1.3.1