| Packages installed | |||
| Package | Version | Description | Install |
| Abaqus | 6.1.4 | Engineering simulation software | software/abaqus-6.14 |
| Annovar | 2018-04 | Functional annotation of genetic variants from high-throughput sequencing data | /opt/exp_soft/annovar-2018-04 |
| AnsysEM | 2020R2 | Electromagnetic | /opt/exp_soft/ansys_inc/AnsysEM20.2 |
| AnsysEM | 19.3 | Electromagnetic | /opt/exp_soft/ansys_inc/AnsysEM19.3 |
| AnsysEM | 19.2 | Electromagnetic | /opt/exp_soft/ansys_inc/AnsysEM19.2 |
| AnsysFluent | 2020R2 | CFD package | /opt/exp_soft/ansys_inc/v202 |
| AnsysFluent | 19.3 | CFD package | /opt/exp_soft/ansys_inc/v193 |
| AnsysFluent | 19.2 | CFD package | /opt/exp_soft/ansys_inc/v192 |
| AnsysFluent | 19.1 | CFD package | /opt/exp_soft/ansys_inc/v191 |
| AnsysFluent | 15.7 | CFD package | /opt/exp_soft/ansys_inc/v150 |
| Astral | 5.6.3 | Unrooted species tree estimation | module load software/Astral-5.6.3 |
| bamtools | 2.5.1 | Toolkit for handling BAM files. | module load software/bamtools-2.5.1 |
| bcftools | 1.9 | Flexible generic format for storing nucleotide sequence alignment | module load software/bcftools-1.9 |
| bcl2fastq | 2.2.0 | Demultiplexes sequencing data and converts BCL files into FASTQ files | module load software/bcl2fastq2-v2.20 |
| BEAGLE | 3.2.0 | Bayesian library for BEAST | via BEAGLE |
| BEAST | 1.10.4 | Phylogenetic analysis with an emphasis on time-scaled trees | module load software/beast-1.10.4 |
| BEAST | 1.8.4 | Phylogenetic analysis with an emphasis on time-scaled trees | module load software/beast-1.8.4 |
| bedtools | 2.29 | Genome arithmetic | module load software/bedtools-2.29 |
| bowtie2 | 2.4.1 | Tool for aligning sequencing reads to long reference sequences | module load software/bowtie2-2.4.1 |
| BWA | 0.7.17 | Burrows-Wheeler Aligner is a program for aligning sequencing reads against a large reference genome | module load software/bwa-0.7.17 |
| cdo | 1.9.6 | Climate Data Operators | module load software/cdo-1.9.6 |
| CellRanger | 3.1.0 | Pipeline for analysing single cell 3' RNA-seq data | module load software/cellranger-3.1.0 |
| cmake | 3.12.4 | software packaging and building tools | module load tools/cmake-3.12.4 |
| diamond | 2.0.1 | Sequence aligner for protein and translated DNA searches | module load software/diamond-2.0.1 |
| emboss | 6.6.0 | Open source software tools for molecular biology | module load software/emboss-6.0.0 |
| ESyS-Particle | 3.0b | Particle-based numerical modelling | module load software/ESyS-Particle-3.0b |
| ESyS-Particle | 2.3.5 | Particle-based numerical modelling | module load software/ESyS-Particle-2.3.5 |
| exonerate | 2.2.0 | Pairwise sequence comparisons | module load software/exonerate-2.2.0 |
| express | 1.5.1 | Streaming fragment assignment and quantification for high-throughput sequencing | module load express-1.5.1 |
| FastQC | 0.11.8 | Quality control application for high throughput sequence data | module load software/FastQC-0.11.8 |
| fftw | 3.3.8 | Fast Fourier Transform library | module load tools/fftw-3.3.8 |
| FreeSurfer | 6.0.1 | Structural and Functional Neuroimaging data | module load software/freesurfer-6.0.1 |
| FreeSurfer | 5.3.0 | Structural and Functional Neuroimaging data | module load software/freesurfer-5.3.0 |
| Gaussian | 9.0 | General purpose computational chemistry software | module load software/gaussian-09 |
| gatk | 4.1.2.0 | The Genome Analysis Toolkit | module load software/gatk-4.1.2.0 |
| gcc | 8.2.0 | Gnu compiler - C and Fortran | module load compilers/gcc820 |
| gnuParallel | 20190722 | Shell tool for executing jobs in parallel - CONTACT HPC ADMINS BEFORE USING!!! | module load software/gnu-parallel-20190722 |
| Gromacs | 2019.1 | Molecular dynamics | module load software/Gromacs-2019.1 |
| Guppy | 3.2.4 | Guppy is a data processing Oxford Nanopore Technologies | module load software/ont-guppy |
| htslib | NA | Tool for accessing common file formats for high-throughput sequencing data | module load tools/htslib |
| hmmer | 3.3.1 | Biosequence analysis using profile hidden Markov models | module load software/hmmer-3.3.1 |
| HyPhy | 2.5.0 | Hypothesis testing using Phylogenies | module load software/HyPhy-2.5.0 |
| HyPhy | 2.3.14 Beta | Hypothesis testing using Phylogenies | module load software/HyPhy-2.3.14B |
| HyPhy | 2.3.12 | Hypothesis testing using Phylogenies | module load software/HyPhy-2.3.12 |
| HyPhy | 2.3.5 | Hypothesis testing using Phylogenies | module load software/HyPhy-2.3.5 |
| iqtree | 2.0.4 | Stochastic algorithm to infer phylogenetic trees by maximum likelihood | module load software/iqtree-2.0.4 |
| iqtree | 1.6.11 | Stochastic algorithm to infer phylogenetic trees by maximum likelihood | module load software/iqtree-1.6.11 |
| Java | 11 | Java language development kit | module load java/jdk-11 |
| Java | 8 | Java language development kit | module load java/jdk-8 |
| Julia | 1.5.2 | Julia compiler | module load compilers/julia-1.5.2 |
| Julia | 1.1.1 | Julia compiler | module load compilers/julia-1.1.1 |
| kallisto | 0.44 | Quantifying abundances of transcripts from RNA-Seq data | module load software/kallisto-0.44 |
| ls-dyna | 10.1.0 | Finite element simulation | module load software/ls-dyna-10.1.0 |
| ls-dyna | 8.1.0 | Finite element simulation | module load software/ls-dyna-8.1.0 |
| mafft | 7.427 | Multiple sequence alignment program for unix-like operating systems | module load software/mafft-7.427 |
| Mathematica | 12.0 | Technical computing | module load software/mathematica-12.0 |
| Matlab | R2020b | Matlab base package | module load software/matlab-R2020b |
| Matlab | R2020b | Parallel Server | Run from desktop |
| Matlab | R2020b | All Toolboxes | Run from matlab |
| Matlab | R2019b | Matlab base package | module load software/matlab-R2019b |
| Matlab | R2019b | Parallel Server | Run from desktop |
| Matlab | R2019b | All Toolboxes | Run from matlab |
| miniconda | 3.7 | Miniconda version of python | module load python/miniconda3 |
| mpich | 3.3 | Message Passing Interface for parallel software | module load mpi/mpich-3.3 |
| Mono | 6.8.0 | Cross platform application development | all worker nodes |
| Monolix | 2019R1 | Mixed effects modeling for pharmacometrics | Pharmacology group only |
| NAMD | 2.13 | Molecular dynamics simulation package | module load software/NAMD-2.13-CUDA |
| NAMD | 2.12 | Molecular dynamics simulation package | module load software/NAMD-2.12-CUDA |
| NAMD | 2.11 | Molecular dynamics simulation package | module load software/NAMD-2.11-CUDA |
| ncbi-blast | 2.9.0 | Basic Local Alignment Search Tool | module load software/ncbi-blast-2.9.0 |
| ncview | 2.1.7 | Visual browser for netcdf files | module load software/ncview-2.1.7 |
| ncview | 2.1.2 | Visual browser for netcdf files | all worker nodes |
| NetCDF-c | 4.6.3 | Network Common Data Form | module load software/netcdf-c-4.6.3 |
| NetCDF-fortran | 4.6.3 | Network Common Data Form | module load software/netcdf-fortran-4.4.5 |
| Nextflow | 20.04 | Data-driven computational pipeline | module load software/nextflow-20.04 |
| Nextflow | 19.04 | Data-driven computational pipeline | module load software/nextflow-19.04 |
| Octave | 4.4.1 | High-level interpreted language for numerical computations | module load software/octave-4.4.1 |
| OpenMPI | 4.0.1 | Message Passing Interface for parallel software | module load mpi/openmpi-4.0.1 |
| OpenMPI | 3.1.2 | Message Passing Interface for parallel software | module load mpi/openmpi-3.1.2 |
| OpenMPI | 1.10.7 | Message Passing Interface for parallel software | module load mpi/openmpi-1.10.7 |
| OpenMPI | 1.8.3 | Message Passing Interface for parallel software | module load mpi/openmpi-1.8.3 |
| paml | 4.9h | Phylogenetic analyses of DNA or protein sequences | module load software/paml-4.9h |
| perl | 5.28.0 | Perl scripting language | module load compilers/perl-5.28 |
| perl | 5.16.3 | Perl scripting language | all worker nodes |
| perl | 5.10.1 | Perl scripting language | module load compilers/perl-5.10 |
| picard | 2.20.1 | Java-based command-line utilities that manipulate SAM files | /opt/exp_soft/picard-2.20.1 |
| plink | 1.07 | Whole genome association analysis toolset | module load software/plink-1.07 |
| Python | 2.7.14 | Anaconda version of python | module load python/anaconda-python-2.7 |
| Python | 3.7.1 | Anaconda version of python | module load python/anaconda-python-3.7 |
| Quantum Espresso | 6.4.1 | Electronic-structure calculations and materials modeling at the nanoscale | module load software/qe-6.4.1 |
| QIIME 2 | 2020.8 | Microbiome analysis package | module load python/miniconda3-qiime2 |
| R | 4.0.1 | Statistical computing and graphics | module load software/R-4.0.1 |
| R | 3.6.0 | Statistical computing and graphics | module load software/R-3.6.0 |
| R | 3.5.3 | Statistical computing and graphics | module load software/R-3.5.3 |
| R | 3.5.2 | Statistical computing and graphics | module load software/R-3.5.2 |
| R | 3.5.1 | Statistical computing and graphics | module load software/R-3.5.1 |
| RAxML | 8.2 | Maximum Likelihood based inference of large phylogenetic trees | module load software/RAxML-8.2 |
| RSEM | 1.3.3 | Accurate quantification of gene and isoform expression from RNA-Seq data | module load software/RSEM-1.3.3 |
| salmon | 1.2.1 | Transcript quantification from RNA-seq data | module load software/salmon-1.2.1 |
| salmon | 1.2.0 | Transcript quantification from RNA-seq data | module load software/salmon-1.2.0 |
| samtools | 1.9 | Flexible generic format for storing nucleotide sequence alignment | module load software/samtools-1.9 |
| Scala | 2.12.8 | Multi-paradigm programming language | module load compile/scala-lang |
| Singularity | 3.0.1 | Containerization environment | all worker nodes |
| snpEff | 4.3 | Fast variant effect predictor for genomic data | /opt/exp_soft/snpEff-4.3/ |
| SortaDate | NA | Genetic analysis | module load software/sorta |
| SPAdes | 3.13.0 | St. Petersburg genome assembler | software/SPAdes-3.13.0 |
| SRAtoolkit | 2.9.6 | A collection of tools and libraries for using data in the INSDC Sequence Read Archives | module load software/sratoolkit-2.9.6 |
| Stata | 13 | Statistics Graphics and Data Management | module load software/stata-13 |
| TensorFlow | 1.12 CPU version | Machine learning framework | module load software/TensorFlow-CPU-py2 or 3 |
| TensorFlow | 1.12 GPU version | Machine learning framework | module load software/TensorFlow-GPU-py2 or 3 |
| Texlive/Latex | 2020 | TeX typesetting system | module load software/texlive2020 |
| TransDecoder | 5.5.0 | Find Coding Regions Within Transcripts | module load software/TransDecoder-v5.5.0 |
| trimAL | 1.2 | Automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment | module load software/trimAL-1.2 |
| Trimmomatic | 0.39 | A flexible read trimming tool for Illumina NGS data | module load software/Trimmomatic-0.39 |
| Trinity | 2.10.0 | RNA-Seq de novo transcriptome assembly | module load software/trinity-2.10.0 |
| Trinotate | 3.2.1 | Transcriptome and protein data search | module load software/Trinotate-v3.2.1 |
| varscan | 2.3.9 | Variant detection in massively parallel sequencing | /opt/exp_soft/varscan-2.3.9 |
| vcflib | NA | C++ library and cmdline tools for parsing and manipulating VCF files | module load software/vcflib |
| vcftools | 0.1.16 | Maps short reads to a reference genome | module load software/vcftools-0.1.16 |
| VMD | 1.9.3 | Visual Molecular Dynamics | module load software/vmd-1.9.3 |
| VMSI | NA | VMSI MicroCosm | module load software/vmsi |