Supported Applications

For more information on environment-modules see Finding Software.

On Mahuika, and Ancillary nodes (both Mahuika and Māui) software packages are provided using 'Lmod' an implementation of Environment Modules with additional features.
A list of available software can be obtained with the module spider command.

On Māui (XC50), software packages are provided using traditional Environment Modules. No modules are loaded by default.
A list of available software can be obtained with the module avail command.

Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.

Available Modules

module load ABAQUS/2020
Links
Licence

ABAQUS is proprietary software.

Access to a valid licence token is required to run ABAQUS.

Institution Faculty Uptime
University of Auckland Faculty of Engineering 98%
University of Waikato 96%

Mass screening of contigs for antimicrobial and virulence genes

Available Modules

module load ABRicate/1.0.0-GCC-11.3.0-Perl-5.34.1
Links

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

Available Modules

module load ABySS/2.2.5-gimpi-2020a
Links

ACTC converts independent triangles into triangle strips or fans.

Available Modules

module load ACTC/1.1-GCCcore-9.2.0
Links

Available Modules

module load ADAM/latest
Links

Suite of tools to handle gene annotations in any GTF/GFF format.

Available Modules

module load AGAT/1.0.0-gimkl-2022a-Perl-5.34.1-R-4.2.1
Links

Alignment of sequences with structural variants.

Available Modules

module load AGE/2017-GCC-7.4.0-serial
Links

Collection of tools for genome assembly

Available Modules

module load AMOS/3.1.0-GCC-11.3.0
Links

NCBI Antimicrobial Resistance Gene Finder Plus

Available Modules

module load AMRFinderPlus/3.10.45-GCC-11.3.0
Links

Calculate the bidirectional average nucleotide identity (gANI) and Alignment Fraction (AF) between two genomes.

Available Modules

module load ANIcalculator/1.0-GCC-11.3.0
Links

Efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes .

Available Modules

module load ANNOVAR/2020Oct01-GCC-9.2.0-Perl-5.30.1
Links

A bundle of computer-aided engineering software including Fluent and CFX.

Available Modules

module load ANSYS/19.2
Links
Licence

ANSYS is proprietary software.

Access to a valid licence token is required to run ANSYS.

Institution Faculty Uptime
University of Auckland Faculty of Engineering 88%
Orbis Diagnostics 100%
Auckland University of Technology Faculty of Engineering 88%
University of Waikato 88%
University of Canterbury 99%
University of Otago 99%

ANother Tool for Language Recognition

Available Modules

module load ANTLR/2.7.7-GCC-7.4.0

Warning

Links

ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.

Available Modules

module load ANTs/2.3.5-gimkl-2020a
Links

AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0

Available Modules

module load AOCC/4.0.0-GCC-11.3.0
Links

Optimized version of FFTW for AMD EPYC family of processors..

Available Modules

module load AOCL-BLIS/4.0-GCC-11.3.0
Links

Optimized version of FFTW for AMD EPYC family of processors.

Available Modules

module load AOCL-FFTW/4.0-gompi-2022a
Links

Optimized version of ScaLAPACK for AMD EPYC family of processors.

Available Modules

module load AOCL-ScaLAPACK/4.0-gompi-2022a
Links

Apache Portable Runtime (APR) libraries.

Available Modules

module load APR/1.6.5
Links

Apache Portable Runtime (APR) util libraries.

Available Modules

module load APR-util/1.6.1

Warning

Links

Available Modules

module load ARCSI/latest
Links

Antimicrobial Resistance Identification By Assembly

Available Modules

module load ARIBA/2.14.6-gimkl-2022a-Python-3.10.5
Links

a pArallel Server for Adaptive GeoInformation

Available Modules

module load ASAGI/20240327-foss-2023a
Links

ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications.

Available Modules

module load ATK/2.36.0-GCCcore-9.2.0
Links

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

Available Modules

module load AUGUSTUS/3.4.0-gimkl-2020a
Links

Collection of C++ library code designed to augment the C++ standard library.

Available Modules

module load Abseil/20230125.3-GCC-11.3.0
Links

Ssearches for and removes remnant adapter sequences from High-Throughput Sequencing data.

Available Modules

module load AdapterRemoval/2.3.1-GCCcore-7.4.0
Links

AdaptiveCpp (formerly hipSYCL) is a SYCL implementation targeting CPUs and GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP

Available Modules

module load AdaptiveCpp/23.10.0-GCC-12.3.0-CUDA-12.2.2
Links

Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain

Available Modules

module load Advisor/2020_update1
Links

AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known

Available Modules

module load AlphaFold/2.3.2
Links

AlphaFold2 databases

Available Modules

module load AlphaFold2DB/2022-06
Links

Overrides the MKL internal utility function mkl_serv_intel_cpu_true so that AVX2 optimised kernels will be used, even when running on an AMD CPU.

Available Modules

module load AlwaysIntelMKL/1.0
Links

Available Modules

module load Amber/latest
Links
Licence

Amber is proprietary software.

Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. IMPORTANT: This version of Anaconda Python comes with Intel MKL support to speed up certain types of mathematical computations, such as linear algebra or FFT. The module sets MKL_NUM_THREADS=1 to run MKL on a single thread by default, avoiding accidental oversubscription of cores. The number of threads can be increased for large problems, please refer to the Intel MKL documentation for guidance.

Available Modules

module load Anaconda3/2021.05-gimkl-2020a

Warning

Links

Available Modules

module load Anaconda3-Geo/latest
Links

Available Modules

module load Anaconda3-Geo2/latest
Links

Available Modules

module load Anaconda3_Geo2/latest
Links

Apptainer is a portable application stack packaging and runtime utility.

Available Modules

module load Apptainer/1.2.5
Links

C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use.

Available Modules

module load Armadillo/10.5.3-gimkl-2020a
Links

Apache Arrow, a cross-language development platform for in-memory data.

Available Modules

module load Arrow/8.0.0-GCCcore-11.3.0
Links

IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows.

Available Modules

module load Aspera-CLI/3.9.6.1467.159c5b1
Links

Available Modules

module load Augustus/latest
Links

OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units.

Available Modules

module load AutoDock-GPU/1.5.3-GCC-11.3.0-CUDA-11.6.2
Links

AutoDock Vina is an open-source program for doing molecular docking.

Available Modules

module load AutoDock_Vina/1.1.2_linux_x86
Links

A collection of more than 500 macros for GNU Autoconf

Available Modules

module load Autoconf-archive/2023.02.20
Links

BBMap short read aligner, and other bioinformatic tools.

Available Modules

module load BBMap/38.95-gimkl-2020a
Links

Manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.

Available Modules

module load BCFtools/1.12-GCC-9.2.0

Warning

Links

Converts per cycle binary data output by Illumina sequencers containing basecall files and quality scores to per read FASTQ files

Available Modules

module load BCL-Convert/4.0.3

Warning

Links

Bayesian MCMC phylogenetic analysis of molecular sequences for reconstructing phylogenies and testing evolutionary hypotheses.

Available Modules

module load BEAST/2.6.6
Links

BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.

Available Modules

module load BEDOPS/2.4.41-gimkl-2022a
Links

The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.

Available Modules

module load BEDTools/2.28.0-gimkl-2018b
Links

BEEF is a library implementing the Bayesian Error Estimation Functional, a description of which can be found here: http://dx.doi.org/10.1103/PhysRevB.85.235149

Available Modules

module load BEEF/0.1.1-r16-intel-2020a
Links

Collection of code for Bayesian genomic cline analyses.

Available Modules

module load BGC-Bayesian-genomic-clines/1.03-gompi-2023a
Links

Available Modules

module load BLASR/latest
Links

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.

Available Modules

module load BLAST/2.9.0-gimkl-2018b
Links

BLAST databases downloaded from NCBI.

Available Modules

module load BLASTDB/2024-07
Links

BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.

Available Modules

module load BLAT/3.5-gimkl-2018b

Warning

Links

BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.

Available Modules

module load BLIS/0.9.0-GCC-11.3.0
Links

The BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis

Available Modules

module load BOLT-LMM/2.4
Links

BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.

Available Modules

module load BRAKER/2.1.6-gimkl-2020a-Perl-5.30.1-Python-3.8.2

Warning

Links

Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

Available Modules

module load BUSCO/4.0.5-gimkl-2020a
Links

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.

Available Modules

module load BWA/0.7.15-gimkl-2017a

Warning

Links

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

Available Modules

module load BamTools/2.5.1-gimkl-2018b
Links

Bandage is a program for visualising de novo assembly graphs

Available Modules

module load Bandage/0.8.1_Centos
Links

Basilisk is a Free Software program for the solution of partial differential equations on adaptive Cartesian meshes.

Available Modules

module load Basilisk/20200620-gimpi-2020
Links

Genome-Wide Scan for Adaptive Differentiation and Association Analysis with population-specific covariables

Available Modules

module load BayPass/2.31-intel-2022a
Links

Identify candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.

Available Modules

module load BayeScan/2.1-GCCcore-7.4.0
Links

Program for inference of recent immigration rates between populations using unlinked multilocus genotypes

Available Modules

module load BayesAss/3.0.4-GCC-9.2.0
Links

Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.

Available Modules

module load Bazel/3.4.1-GCCcore-9.2.0

Warning

Links

Package for phasing genotypes and for imputing ungenotyped markers.

Available Modules

module load Beagle/5.0-12Jul19.0df
Links

Available Modules

module load BerkeleyGW/latest
Links

Available Modules

module load Berkeley_UPC/latest
Links

Constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs).

Available Modules

module load BiG-SCAPE/1.1.5-gimkl-2022a-Python-3.11.3
Links

Highly parallel construction, indexing and querying of colored and compacted de Bruijn graphs.

Available Modules

module load Bifrost/1.0.4-GCC-9.2.0

Warning

Links

Read BigWig and BigBed genome feature databases

Available Modules

module load Bio-DB-BigFile/1.07-GCC-9.2.0-Perl-5.30.1-mt
Links

Read files using HTSlib including BAM/CRAM, Tabix and BCF database files

Available Modules

module load Bio-DB-HTS/3.01-GCC-11.3.0-Perl-5.34.1
Links

Available Modules

module load BioConductor/latest
Links

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

Available Modules

module load BioPP/2.4.1-GCC-9.2.0
Links

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

Available Modules

module load Bismark/0.22.3-gimkl-2018b
Links

Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.

Available Modules

module load Bison/3.0.4-GCC-5.4.0
Links

Blender provides a pipeline for 3D modeling, rigging, animation, simulation, rendering, compositing, motion tracking, video editing and 2D animation. This particular build of Blender provides a Python package 'bpy' rather than the stand-alone application.

Available Modules

module load BlenderPy/2.93.1-gimkl-2020a-Python-3.9.5

Warning

Links

Boost provides free peer-reviewed portable C++ source libraries.

Available Modules

module load Boost/1.76.0-intel-2022a
Links

Ultrafast, memory-efficient short read aligner.

Available Modules

module load Bowtie/0.12.8
Links

Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Available Modules

module load Bowtie2/2.4.1-GCC-9.2.0
Links

A platform for running big bioinformatics jobs that consist of a series of processing stages

Available Modules

module load Bpipe/0.9.9.8

Warning

Links

Hghly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

Available Modules

module load Bracken/2.6.0-GCCcore-9.2.0

Warning

Links

Genome-wide detection of structural variants from next generation paired-end sequencing reads.

Available Modules

module load BreakDancer/1.4.5-gimkl-2017a.lua
Links

Nucleotide-resolution analysis of structural variants

Available Modules

module load BreakSeq2/2.2-gimkl-2018b-Python-2.7.16

Warning

Links

Clozure CL (often called CCL for short) is a free Common Lisp implementation

Available Modules

module load CCL/1.12-GCCcore-9.2.0

Warning

Links

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

Available Modules

module load CD-HIT/4.8.1-GCC-11.3.0
Links

CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.

Available Modules

module load CDO/1.9.8-gimpi-2020a
Links

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

Available Modules

module load CFITSIO/3.45-GCCcore-7.4.0
Links

The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.

Available Modules

module load CGAL/4.13-GCCcore-7.4.0
Links

CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

Available Modules

module load CMake/3.22.1
Links

Copy Number Variation discovery and genotyping from depth of read mapping.

Available Modules

module load CNVnator/0.4-GCC-7.4.0
Links

Python package and command line tool for CNV/CNA analysis from depth-of-coverage by mapped read

Available Modules

module load CNVpytor/1.0-gimkl-2020a-Python-3.8.2
Links

COMSOL is a multiphysics solver that provides a unified workflow for electrical, mechanical, fluid, and chemical applications.

Available Modules

module load COMSOL/5.6
Links
Licence

COMSOL is proprietary software.

Access to a valid licence token is required to run COMSOL.

Institution Faculty Uptime
University of Auckland Physics 98%
Auckland Bioengineering Institute Implantable devices group 98%
University of Auckland Faculty of Engineering 98%
University of Auckland Deptartment of Engineering Science 98%
University of Auckland Deptartment of Engineering Science 98%
University of Otago 99%
University of Canterbury 100%

Program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.

Available Modules

module load CONCOCT/1.1.0-gimkl-2020a-Python-3.8.2
Links

CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.

Available Modules

module load CP2K/8.2-intel-2022a-PLUMED-2.7.2
Links

The CPMD code is a parallelized plane wave / pseudopotential implementation of DFT, particularly designed for ab-initio molecular dynamics.

Available Modules

module load CPMD/4.3-foss-2023a
Links

A tool for quick quality assessment of cram and bam files, intended for long read sequencing

Available Modules

module load CRAMINO/0.9.7-GCC-11.3.0
Links

C++ Thread Pool Library

Available Modules

module load CTPL/0.0.2

Warning

Links

CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.

Available Modules

module load CUDA/11.0.2
Links

Automated testing framework for C.

Available Modules

module load CUnit/2.1-3-GCCcore-9.2.0

Warning

Links

Available Modules

module load Cannoli/latest
Links

Sequence assembler designed for high-noise single-molecule sequencing.

Available Modules

module load Canu/2.2-GCC-11.3.0
Links

Fast data interchange format and capability-based RPC system.

Available Modules

module load CapnProto/0.8.0-GCCcore-9.2.0
Links

A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch)

Available Modules

module load Catch2/2.13.4

Warning

Links

Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.

Available Modules

module load CellRanger/6.1.2
Links

Classifier for metagenomic sequences

Available Modules

module load Centrifuge/1.0.4.1-GCC-12.3.0
Links

C++11 serialization library

Available Modules

module load Cereal/1.3.0
Links

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.

Available Modules

module load CheckM/1.2.1-gimkl-2022a-Python-3.10.5
Links

Rapid assessment of genome bin quality using machine learning

Available Modules

module load CheckM2/1.0.1-Miniconda3
Links

Assess the quality of metagenome-assembled viral genomes.

Available Modules

module load CheckV/0.6.0-gimkl-2020a-Python-3.8.2

Warning

Links

A tool to circularize genome assemblies

Available Modules

module load Circlator/1.5.5-gimkl-2022a-Python-3.10.5
Links

Package for visualizing data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.

Available Modules

module load Circos/0.69-9-GCC-9.2.0
Links

Syumphonizing pileup and full-alignment for high-performance long-read variant calling.

Available Modules

module load Clair3/0.1.12-Miniconda3
Links

C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.

Available Modules

module load Clang/17.0.6-GCC-12.3.0-CUDA-12.2.2
Links

Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms

Available Modules

module load Clustal-Omega/1.2.4-GCC-11.3.0
Links

ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.

Available Modules

module load ClustalW2/2.1-gimkl-2017a

Warning

Links

Clusters contigs and counts reads from de novo assembled transcriptomes.

Available Modules

module load Corset/1.09-GCC-9.2.0

Warning

Links

DNA read coverage and relative abundance calculator focused on metagenomics applications

Available Modules

module load CoverM/0.7.0-GCC-12.3.0
Links

C++ port of the JUnit framework for unit testing.

Available Modules

module load CppUnit/1.13.2-GCCcore-7.4.0

Warning

Links

Available Modules

module load CubeGUI/latest
Links

Cube general purpose C++ library component and command-line tools.

Available Modules

module load CubeLib/4.4.4-GCCcore-9.2.0
Links

Cube high-performance C writer library component.

Available Modules

module load CubeWriter/4.5-GCCcore-9.2.0
Links

Transcript assembly, differential expression, and differential regulation for RNA-Seq

Available Modules

module load Cufflinks/2.2.1-gimkl-2017a
Links

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Available Modules

module load Cytoscape/2.7.0

Warning

Links

D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.

Available Modules

module load D-Genies/1.5.0-gimkl-2022a-Python-3.11.3
Links

DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.

Available Modules

module load DAS_Tool/1.1.5-gimkl-2022a-R-4.2.1
Links

Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.

Available Modules

module load DB/6.2.23-GCCcore-7.4.0
Links

Available Modules

module load DBG2OLC/latest
Links

D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed.

Available Modules

module load DBus/1.13.8-GCCcore-7.4.0
Links

Generally Applicable Atomic-Charge Dependent London Dispersion Correction.

Available Modules

module load DFT-D4/3.5.0-foss-2023a
Links

Sequence aligner for protein and translated DNA searches

Available Modules

module load DIAMOND/2.1.9-GCC-11.3.0
Links

Assembler suitable for large genomes based on Illumina reads of length 250 or longer.

Available Modules

module load DISCOVARdenovo/52488

Warning

Links

Available Modules

module load DMTCP/latest
Links

Tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs..

Available Modules

module load DRAM/1.3.5-Miniconda3
Links

Tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.

Available Modules

module load DaliLite/5.0-iimpi-2020a

Warning

Links

A tool that can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets.

Available Modules

module load DeconSeq/0.4.3
Links

Available Modules

module load DeePMD-kit/2.1.1
Links

Efficient method for 3D markerless pose estimation based on transfer learning with deep neural networks.

Available Modules

module load DeepLabCut/2.3.5
Links

Integrated simulation of sediment transport and morphology, waves, water quality and ecology.

Available Modules

module load Delft3D/141732-intel-2022a
Links

3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments

Available Modules

module load Delft3D_FM/68673-intel-2020a
Links

Structural variant discovery by integrated paired-end and split-read analysis

Available Modules

module load Delly/1.1.3
Links

Available Modules

module load DendroPy/latest
Links

High-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.

Available Modules

module load Dorado/0.3.2
Links

Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.

Available Modules

module load Doxygen/1.8.17-GCCcore-9.2.0
Links

Fast calculation of the ABBA-BABA statistics across many populations/species

Available Modules

module load Dsuite/20210718-intel-compilers-2022.0.2
Links

Automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries.

Available Modules

module load EDTA/2.1.0
Links

The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.

Available Modules

module load EIGENSOFT/7.2.1-gimkl-2018b
Links

Eigenvalue SoLvers for Petaflop-Applications .

Available Modules

module load ELPA/2023.11.001-foss-2023a
Links

Available Modules

module load EMAN/latest
Links

Greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes

Available Modules

module load EMAN2/2.99.47-gpu
Links

EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.

Available Modules

module load EMBOSS/6.6.0-gimkl-2020a
Links

Available Modules

module load EMIRGE/latest
Links

R package for integrated construction of Ecological Niche Models.

Available Modules

module load ENMTML/2021-06-24-gimkl-2020a-R-4.1.0

Warning

Links

The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models.

Available Modules

module load ESMF/7.1.0r-intel-2018b
Links

A Python framework for the analysis and visualization of phylogenetic trees

Available Modules

module load ETE/3.1.1-gimkl-2018b-Python-3.7.3
Links

Available Modules

module load EasyBuild/4.7
Links

Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

Available Modules

module load Eigen/3.3.9
Links

Available Modules

module load Elmer/latest
Links

Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels.

Available Modules

module load Embree/3.5.1-GCCcore-7.4.0
Links

Available Modules

module load EnergyPlus/latest
Links

Available Modules

module load ErlangOTP/latest
Links

Completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes. Also condatains smetana, carveme and memote .

Available Modules

module load EukRep-EukCC/0.6.7-2.1.0-Miniconda3
Links

Bayesian tree inference, particularly suitable for large-scale analyses.

Available Modules

module load ExaBayes/1.5.1-gimpi-2020a
Links

Exascale Maximum Likelihood for phylogenetic inference using MPI.

Available Modules

module load ExaML/3.0.22-gimkl-2020a
Links

Tool for estimating repeat sizes

Available Modules

module load ExpansionHunter/5.0.0
Links

Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches

Available Modules

module load Extrae/3.8.3-intel-2020a

Warning

Links

Falcon: a set of tools for fast aligning long reads for consensus and assembly

Available Modules

module load FALCON/1.8.8-gimkl-2020a-Python-2.7.18
Links

Tools for Short-Reads FASTA/FASTQ files preprocessing.

Available Modules

module load FASTX-Toolkit/0.0.14-GCC-11.3.0
Links

FCM Build - A powerful build system for modern Fortran software applications. FCM Version Control - Wrappers to the Subversion version control system, usage conventions and processes for scientific software development.

Available Modules

module load FCM/2019.09.0-GCC-12.3.0
Links

Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires.

Available Modules

module load FDS/6.7.5-1526-intel-2020a

Warning

Links

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.

Available Modules

module load FFTW/3.3.10-GCC-12.3.0
Links

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.

Available Modules

module load FFTW.MPI/3.3.10-gompi-2023a
Links

A complete, cross-platform solution to record, convert and stream audio and video.

Available Modules

module load FFmpeg/5.1.1-GCC-11.3.0
Links

An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters.

Available Modules

module load FIGARO/1.1.2-gimkl-2022a-Python-3.11.3
Links

FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.

Available Modules

module load FLTK/1.3.5-GCCcore-9.2.0
Links

Available Modules

module load FPM/latest
Links

FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications.

Available Modules

module load FTGL/2.1.3-rc5-GCCcore-7.4.0
Links

Tool for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).

Available Modules

module load FastANI/1.33-intel-2020a
Links

FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.

Available Modules

module load FastME/2.1.6.1-gimkl-2018b
Links

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

Available Modules

module load FastQC/0.12.1
Links

FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

Available Modules

module load FastQ_Screen/0.15.1-GCC-9.2.0-Perl-5.30.1
Links

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

Available Modules

module load FastTree/2.1.11-GCC-12.3.0
Links

A Perl version of the rename utility, with support for regular expressions.

Available Modules

module load File-Rename/1.13-GCC-9.2.0
Links

Tool for filtering long reads by quality.

Available Modules

module load Filtlong/0.2.0
Links

Identifies the FimH type in total or partial sequenced isolates of E. coli..

Available Modules

module load FimTyper/1.0.1-GCC-11.3.0-Perl-5.34.1

Warning

Links

FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.

Available Modules

module load FlexiBLAS/3.3.1-GCC-12.3.0
Links

Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.

Available Modules

module load Flye/2.9.3-gimkl-2022a-Python-3.11.3
Links

Available Modules

module load FoX/latest
Links

FragGeneScan is an application for finding (fragmented) genes in short reads.

Available Modules

module load FragGeneScan/1.31-gimkl-2018b
Links

Genetic variant detector designed to find polymorphisms smaller than the length of a short-read sequencing alignment.

Available Modules

module load FreeBayes/1.3.2-GCC-9.2.0
Links

FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.

Available Modules

module load FreeSurfer/7.2.0-centos7_x86_64
Links

FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.

Available Modules

module load FreeXL/1.0.2-gimkl-2017a
Links

Free Implementation of the Unicode Bidirectional Algorithm.

Available Modules

module load FriBidi/1.0.12-GCC-12.3.0
Links

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

Available Modules

module load GATK/3.8-1
Links

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).

Available Modules

module load GCC/5.4.0
Links

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).

Available Modules

module load GCCcore/5.4.0
Links

Interface to Gd Graphics Library

Available Modules

module load GD/2.76-GCC-11.3.0-Perl-5.34.1
Links

GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful command-line utilities for data translation and processing. NOTE: The GDAL IO cache by default uses 5% of total memory. This seems not necessary. This module sets GDAL_CACHEMAX=256 (256MB), which should have no performance impact. Feel free to change if necessary, using 'export GDAL_CACHEMAX=xxx' (in your job script) after loading the GDAL module.

Available Modules

module load GDAL/3.0.4-gimkl-2020a.lua
Links

Genome-wide Efficient Mixed Model Association

Available Modules

module load GEMMA/0.98.5-GCC-12.3.0
Links

GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)

Available Modules

module load GEOS/3.11.3-GCC-12.3.0
Links

OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.

Available Modules

module load GLM/0.9.9.8
Links

GNU Linear Programming Kit is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems.

Available Modules

module load GLPK/5.0-GCCcore-11.3.0
Links

GLib is one of the base libraries of the GTK+ project

Available Modules

module load GLib/2.53.7-GCCcore-7.4.0
Links

C++ bindings for Glib

Available Modules

module load GLibmm/2.49.7-GCCcore-9.2.0.lua
Links

Available Modules

module load GLnexus/latest
Links

GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program

Available Modules

module load GMAP-GSNAP/2021-12-17-GCC-11.3.0
Links

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.

Available Modules

module load GMP/6.2.1-GCCcore-12.3.0
Links

A genetic algorithm for docking flexible ligands into protein binding sites

Available Modules

module load GOLD/2020

Warning

Links
Licence

GOLD is proprietary software.

GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.

Available Modules

module load GObject-Introspection/1.72.0-GCC-11.3.0

Warning

Links

GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions.

Available Modules

module load GPAW/24.1.0-foss-2023a
Links

The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization

Available Modules

module load GRASS/7.6.1-gimkl-2018b-Python-2.7.16
Links

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

Available Modules

module load GRIDSS/2.13.2-gimkl-2020a
Links

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI binaries.

Available Modules

module load GROMACS/2020.5-intel-2020a-cuda-11.0.2-hybrid
Links

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.

Available Modules

module load GSL/2.7-GCC-12.3.0
Links

GStreamer plug-ins and elements.

Available Modules

module load GST-plugins-base/1.16.2-GCC-9.2.0
Links

library for constructing graphs of media-handling components..

Available Modules

module load GStreamer/1.16.2-GCC-9.2.0
Links

A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Available Modules

module load GTDB-Tk/2.1.0-gimkl-2020a-Python-3.9.9
Links

GTK+ is the primary library used to construct user interfaces in GNOME.

Available Modules

module load GTK+/3.24.23-GCC-9.2.0
Links

GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.

Available Modules

module load GTS/121130-GCCcore-7.4.0
Links

Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation.

Available Modules

module load GUSHR/2020-09-28-gimkl-2022a-Python-3.11.3
Links

Available Modules

module load Gaussian/09-C
Links
Licence

Gaussian is proprietary software.

The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.

Available Modules

module load Gdk-Pixbuf/2.42.8-GCC-11.3.0
Links

Eukaryotic gene prediction suite with automatic training

Available Modules

module load GeneMark-ES/4.71-GCC-11.3.0
Links

Generates circular genome representations for complete, draft, and multiple bacterial and archaeal genomes.

Available Modules

module load GenoVi/0.2.16-Miniconda3
Links

GenomeThreader is a software tool to compute gene structure predictions.

Available Modules

module load GenomeThreader/1.7.3-Linux_x86_64-64bit
Links

Available Modules

module load Gerris/latest
Links

Toolkit to assemble organelle genome from genomic skimming data.

Available Modules

module load GetOrganelle/1.7.7.0-gimkl-2022a
Links

Gene finder based on a Generalized Hidden Markov Model.

Available Modules

module load GlimmerHMM/3.0.4c-GCC-9.2.0
Links

An open source programming language

Available Modules

module load Go/1.11.5

Warning

Links

Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.

Available Modules

module load Graphviz/2.42.2-GCC-9.2.0
Links

Genealogies Unbiased By recomBinations In Nucleotide Sequences

Available Modules

module load Gubbins/3.2.2-gimkl-2022a-Python-3.10.5
Links

Available Modules

module load Guile/latest
Links

HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.

Available Modules

module load HDF/4.2.15-GCCcore-9.2.0
Links

HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.

Available Modules

module load HDF5/1.12.2-iimpi-2022a
Links

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).

Available Modules

module load HISAT2/2.2.1-gimkl-2020a
Links

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.

Available Modules

module load HMMER/3.3.2-GCC-9.2.0
Links

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.

Available Modules

module load HMMER2/2.3.2-GCC-9.2.0
Links

Pipeline which focuses on screening MALT data for the presence of a user-specified list of target species.

Available Modules

module load HOPS/0.33

Warning

Links

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

Available Modules

module load HTSeq/0.13.5-gimkl-2020a-Python-3.9.5
Links

A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix

Available Modules

module load HTSlib/1.12-GCCcore-9.2.0
Links

HarfBuzz is an OpenType text shaping engine.

Available Modules

module load HarfBuzz/4.4.1-GCC-11.3.0
Links

HPC GridRunner is a simple command-line interface to high throughput computing using a variety of different grid computing platforms, including LSF, SGE, SLURM, and PBS.

Available Modules

module load HpcGridRunner/20181005
Links

Pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data.

Available Modules

module load Humann/3.0.0.alpha.3
Links

Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment.

Available Modules

module load HybPiper/2.0.1rc-Miniconda3
Links

Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.

Available Modules

module load Hypre/2.21.0-gimkl-2022a
Links

C/C++ and Java libraries providing Unicode and Globalization support for software applications.

Available Modules

module load ICU/50.2-GCCcore-9.2.0
Links

Available Modules

module load IDBA/latest
Links

IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.

Available Modules

module load IDBA-UD/1.1.3-GCC-11.3.0
Links

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data

Available Modules

module load IGV/2.5.0
Links

Genotype imputation and haplotype phasing.

Available Modules

module load IMPUTE/2.3.2
Links

Efficient phylogenomic software by maximum likelihood

Available Modules

module load IQ-TREE/2.2.0.5-gimpi-2022a
Links

Available Modules

module load IQmol/2.11
Links
Licence

IQmol is proprietary software.

R packages for providing R kernel for Jupyter.

Available Modules

module load IRkernel/1.0.1-gimkl-2018b
Links

Intelligent Storage Acceleration Library

Available Modules

module load ISA-L/2.30.0
Links

Available Modules

module load IVE/latest
Links

Create, edit, compose, or convert bitmap images

Available Modules

module load ImageMagick/7.0.9-5-GCCcore-9.2.0
Links

Infernal ('INFERence of RNA ALignment') is for searching DNA sequence databases for RNA structure and sequence similarities.

Available Modules

module load Infernal/1.1.4-GCC-11.3.0
Links

Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications

Available Modules

module load Inspector/2019_update5
Links

Sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource.

Available Modules

module load InterProScan/5.62-94.0-gimkl-2022aPerl-5.34.1-Python-3.11.3
Links

Just Another Gibbs Sampler - a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo.

Available Modules

module load JAGS/4.3.1-gimkl-2022a-mt
Links

A programmer-oriented testing framework for Java.

Available Modules

module load JUnit/4.12-Java-1.8.0_144

Warning

Links

The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.

Available Modules

module load JasPer/2.0.14-GCCcore-7.4.0
Links

Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.

Available Modules

module load Java/17
Links

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.

Available Modules

module load Jellyfish/2.2.10-gimkl-2020a

Warning

Links

JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.

Available Modules

module load JsonCpp/1.9.3-GCCcore-9.2.0
Links

Available Modules

module load Julia/1.1.0

Warning

Links

Available Modules

module load JupyterHub/latest
Links

An extensible environment for interactive and reproducible computing, based on the Jupyter Notebook and Architecture.

Available Modules

module load JupyterLab/2022.7.0-gimkl-2020a-3.4.3
Links

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

Available Modules

module load KAT/2.4.2-gimkl-2018b-Python-3.7.3
Links

KEALib provides an implementation of the GDAL data model. The format supports raster attribute tables, image pyramids, meta-data and in-built statistics while also handling very large files and compression throughout. Based on the HDF5 standard, it also provides a base from which other formats can be derived and is a good choice for long term data archiving. An independent software library (libkea) provides complete access to the KEA image format and a GDAL driver allowing KEA images to be used from any GDAL supported software.

Available Modules

module load KEALib/1.4.15-gimpi-2022a
Links

Disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.

Available Modules

module load KMC/3.1.2rc1-gimkl-2020a-Python-3.8.2
Links

Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments

Available Modules

module load Kaiju/1.8.2-gimkl-2020a-Python-3.9.9-Perl-5.30.1-mt
Links

Collection of tools used by the UCSC genome browser.

Available Modules

module load Kent_tools/20200519-linux.x86_64
Links

KmerGenie estimates the best k-mer length for genome de novo assembly.

Available Modules

module load KmerGenie/1.7051-gimkl-2022a
Links

Semi-HMM-based Nucleic Acid Parser

Available Modules

module load KorfSNAP/2013-11-29-GCC-9.2.0
Links

Taxonomic sequence classifier.

Available Modules

module load Kraken2/2.0.7-beta-gimkl-2017a.lua
Links

Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.

Available Modules

module load KronaTools/2.8.1-GCC-11.3.0-Perl-5.34.1
Links

Library of routines for managing a database.

Available Modules

module load KyotoCabinet/1.2.77-GCCcore-7.4.0

Warning

Links

LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.

Available Modules

module load LAME/3.100-GCCcore-7.4.0
Links

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

Available Modules

module load LAMMPS/23Jun2022-gimkl-2022a-kokkos
Links

LAST finds similar regions between sequences.

Available Modules

module load LAST/1060-gimkl-2020a

Warning

Links

LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

Available Modules

module load LASTZ/1.04.22-GCC-12.3.0
Links

D programming language compiler

Available Modules

module load LDC/1.26.0

Warning

Links

Determines the features most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance

Available Modules

module load LEfSe/1.1.2-gimkl-2022a-R-4.2.1-Python-3.10.5
Links

Alignment-free scaffolding of genome assembly drafts with long reads

Available Modules

module load LINKS/1.8.5-gimkl-2018b
Links

The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.

Available Modules

module load LLVM/14.0.6-GCC-11.3.0-static
Links

LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.

Available Modules

module load LMDB/0.9.29-GCC-11.3.0
Links

Least-squares methods to estimate rates and dates from phylogenies

Available Modules

module load LSD2/2.3-GCC-11.3.0
Links

Highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

Available Modules

module load LTR_retriever/2.9.0-gimkl-2020a
Links

A probabilistic framework for structural variant discovery.

Available Modules

module load LUMPY/0.3.1-gimkl-2020a-Python-3.8.2
Links

Portable lossless data compression library

Available Modules

module load LZO/2.10-GCCcore-9.2.0
Links

Available Modules

module load LegacySystemLibs/7
Links

tiff: Library and tools for reading and writing TIFF data files

Available Modules

module load LibTIFF/4.4.0-GCCcore-11.3.0
Links

Available Modules

module load Libav/latest
Links

Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.

Available Modules

module load Libint/2.6.0-iimpi-2020a-lmax-6-cp2k

Warning

Links

Tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species.

Available Modules

module load Liftoff/1.6.3.2-gimkl-2022a-Python-3.11.3
Links

Color management engine.

Available Modules

module load LittleCMS/2.9-GCCcore-9.2.0
Links

Available Modules

module load Loki/latest
Links

A genome assembly correction and scaffolding pipeline using long reads

Available Modules

module load LongStitch/1.0.4-Miniconda3
Links

GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.

Available Modules

module load M4/1.4.18-GCCcore-7.4.0
Links

Multiple sequence alignment program offering a range of methods.

Available Modules

module load MAFFT/7.505-gimkl-2022a-with-extensions
Links

Tool for gene analysis and generalized gene-set analysis of GWAS data.

Available Modules

module load MAGMA/1.08-GCCcore-9.2.0

Warning

Links

Genome annotation pipeline

Available Modules

module load MAKER/2.31.9-gimkl-2018b

Warning

Links

matio is an C library for reading and writing Matlab MAT files.

Available Modules

module load MATIO/1.5.17-GCCcore-7.4.0
Links

A high-level language and interactive environment for numerical computing.

Available Modules

module load MATLAB/2021b
Links
Licence

MATLAB is proprietary software.

Access to a valid licence token is required to run MATLAB.

Institution Uptime
University of Waikato 98%
National Institute of Water and Atmospheric Research 0%
Institute of Geological and Nuclear Sciences 99%
Massey University 13%
University of Auckland 98%
University of Otago 100%
Victoria University of Wellington 100%
Auckland University of Technology 12%
University of Canterbury 12%
Plant & Food Research 13%

The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.

Available Modules

module load MCL/14.137-gimkl-2018b
Links

The Matlab Compiler Runtime is required for running compiled MATLAB executables without MATLAB itself.

Available Modules

module load MCR/2019a

Warning

Links

An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Available Modules

module load MEGAHIT/1.1.4-gimkl-2018b-Python-2.7.16
Links

Metabolic And Biogeochemistry anaLyses In microbes

Available Modules

module load METABOLIC/4.0-Miniconda3
Links

METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.

Available Modules

module load METIS/5.1.0-GCCcore-9.2.0
Links

MMseqs2: ultra fast and sensitive search and clustering suite

Available Modules

module load MMseqs2/15-6f452-gompi-2023a
Links

Available Modules

module load MOB-suite/latest
Links

MODFLOW is the U.S. Geological Survey modular finite-difference flow model, which is a computer code that solves the groundwater flow equation. The program is used by hydrogeologists to simulate the flow of groundwater through aquifers.

Available Modules

module load MODFLOW/6.2.2-GCC-9.2.0

Warning

Links

The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.

Available Modules

module load MPFR/4.0.2-GCCcore-9.2.0
Links

Available Modules

module load MPICH/latest
Links

Multiple Sequentially Markovian Coalescent, infers population size and gene flow from multiple genome sequences

Available Modules

module load MSMC/1.1.0-GCC-7.4.0

Warning

Links

A parallel sparse direct solver

Available Modules

module load MUMPS/4.10.0-gimkl-2020a-metis-4.0.3
Links

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.

Available Modules

module load MUMmer/4.0.0rc1-GCCcore-11.3.0
Links

MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two.

Available Modules

module load MUSCLE/3.8.31
Links

MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user.

Available Modules

module load MUST/1.6-gimkl-2020a-Python-3.8.2

Warning

Links

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore).

Available Modules

module load MaSuRCA/4.0.5-gimkl-2020a
Links

Magma is a large, well-supported software package designed for computations in algebra, number theory, algebraic geometry and algebraic combinatorics. It provides a mathematically rigorous environment for defining and working with structures such as groups, rings, fields, modules, algebras, schemes, curves, graphs, designs, codes and many others. Magma also supports a number of databases designed to aid computational research in those areas of mathematics which are algebraic in nature. whatis([==[Homepage: http://magma.maths.usyd.edu.au/magma/

Available Modules

module load Magma/Magma-2.26.9

Warning

Links

Mamba is a fast, robust, and cross-platform package manager.

Available Modules

module load Mamba/23.1.0-1
Links

Workflow for effective discovery of SCN loci in flowering plants angiosperms

Available Modules

module load MarkerMiner/1.0-gimkl-2020a-Python-2.7.18
Links

Fast genome and metagenome distance estimation using MinHash

Available Modules

module load Mash/2.3-GCC-11.3.0
Links

Implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences

Available Modules

module load MashMap/3.0.4-Miniconda3
Links

Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.

Available Modules

module load Maven/3.6.0
Links

MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.

Available Modules

module load MaxBin/2.2.7-GCC-11.3.0-Perl-5.34.1
Links

Available Modules

module load Meraculous/latest
Links

Evaluate genome assemblies with k-mers and more

Available Modules

module load Merqury/1.3-Miniconda3
Links

Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. Note that this build enables CPU-based rendering with OpenSWR and LLVM. The module is intended to be used with visualisation software, such as ParaView, on nodes where no GPU hardware is available. Both on-screen and off-screen rendering are supported.

Available Modules

module load Mesa/19.2.1-GCCcore-9.2.0
Links

Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.

Available Modules

module load Meson/0.53.2

Warning

Links

An efficient tool for accurately reconstructing single genomes from complex microbial communities

Available Modules

module load MetaBAT/2.17-GCC-12.3.0
Links

MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.

Available Modules

module load MetaEuk/6-GCC-11.3.0
Links

MetaGeneAnnotator is a gene-finding program for prokaryote and phage.

Available Modules

module load MetaGeneAnnotator/20080819-x86-64
Links

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.

Available Modules

module load MetaPhlAn/4.0.4-gimkl-2022a-Python-3.10.5
Links

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.

Available Modules

module load MetaPhlAn2/2.7.8-gimkl-2018b-Python-3.7.3
Links

Structural-variant caller

Available Modules

module load MetaSV/0.5.4-gimkl-2018b-Python-2.7.16
Links

Available Modules

module load MetaVelvet/latest
Links

Available Modules

module load Metashape/1.6

Warning

Links

Taxonomic classification of rRNA.

Available Modules

module load Metaxa2/2.2.2-gimkl-2020a
Links

MiMiC: A Framework for Multiscale Modeling in Computational Chemistry This package includes mimicpy

Available Modules

module load MiMiC/0.2.0-gimkl-2022a-Python-3.11.3
Links

The MiMiC communication library (MCL) enables communication between external programs coupled through the MiMiC framework.

Available Modules

module load MiMiC-CommLib/2.0.2-gimkl-2022a
Links

A platform for Python-based data analytics

Available Modules