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/2022

module load ABAQUS/2022
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 99%

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

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

Available Modules

module load ABySS/2.2.5-gimpi-2020a

ACTC converts independent triangles into triangle strips or fans.

Available Modules

module load ACTC/1.1-GCCcore-9.2.0

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

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

NCBI Antimicrobial Resistance Gene Finder Plus

Available Modules

module load AMRFinderPlus/3.10.45-GCC-11.3.0

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

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

Available Modules

module load ANSYS/19.2
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 72%
Orbis Diagnostics 100%
Auckland University of Technology Faculty of Engineering 72%
University of Waikato 72%
University of Canterbury 99%
University of Otago 99%

ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions.

Available Modules

module load ANTLR/2.7.7-GCC-11.3.0

module load ANTLR/2.7.7-GCC-7.1.0

Ants is a versatile, easy to use Python library for developing ancillary applications. This package is restricted to the UM user group.

Available Modules

module load ANTS/0.9.0

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

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

Available Modules

module load AOCC/4.0.0-GCC-11.3.0

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

Available Modules

module load AOCL-BLIS/4.0-GCC-11.3.0

Optimized version of FFTW for AMD EPYC family of processors.

Available Modules

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

Optimized version of ScaLAPACK for AMD EPYC family of processors.

Available Modules

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

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

Antimicrobial Resistance Identification By Assembly

Available Modules

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

a pArallel Server for Adaptive GeoInformation

Available Modules

module load ASAGI/20240327-foss-2023a

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

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

Available Modules

module load Abseil/20230125.3-GCC-11.3.0

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

Available Modules

module load AdapterRemoval/2.3.1-GCCcore-7.4.0

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

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/2023.1.0

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

Available Modules

module load AlphaFold/2.3.2

AlphaFold2 databases

Available Modules

module load AlphaFold2DB/2023-04
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

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 Anaconda2/2019.10-GCC-7.1.0

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.

Available Modules

module load Anaconda3/2021.05-gimkl-2020a

module load Anaconda3/2020.02-GCC-7.1.0

Apptainer is a portable application stack packaging and runtime utility.

Available Modules

module load Apptainer/1.3.1

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

Available Modules

module load Armadillo/11.1.1-gimkl-2022a

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

Available Modules

module load Arrow/14.0.1-GCC-12.3.0

module load Arrow/8.0.0-GCCcore-9.2.0

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

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

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

Available Modules

module load AutoDock_Vina/1.1.2_linux_x86

A collection of more than 500 macros for GNU Autoconf

Available Modules

module load Autoconf-archive/2023.02.20

BBMap short read aligner, and other bioinformatic tools.

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

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/4.2.4

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

Available Modules

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

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

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

Collection of code for Bayesian genomic cline analyses.

Available Modules

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

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.

BLAST databases downloaded from NCBI.

Available Modules

module load BLASTDB/2024-04
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

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

Available Modules

module load BLIS/4.0-GCC-11.3.0-amd

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

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

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

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
Links

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

Available Modules

module load BamTools/2.5.2-GCC-11.3.0

Bandage is a program for visualising de novo assembly graphs

Available Modules

module load Bandage/0.8.1_Centos

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

Available Modules

module load Basilisk/20180226-gimpi-2018b

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

Available Modules

module load BayPass/2.31-intel-2022a

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

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

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

Available Modules

Package for phasing genotypes and for imputing ungenotyped markers.

Available Modules

module load Beagle/5.4-22Jul22.46e

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

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

Read BigWig and BigBed genome feature databases

Available Modules

module load Bio-DB-BigFile/1.07-GCC-11.3.0-Perl-5.34.1

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

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

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

Available Modules

module load Bismark/0.24.0-GCC-11.3.0

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/3.3.2-GCCcore-7.4.0

module load Bison/3.0.4-GCC-7.1.0

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

Ultrafast, memory-efficient short read aligner.

Available Modules

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

Available Modules

module load Bowtie2/2.4.5-GCC-11.3.0

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

Available Modules

module load Bpipe/0.9.9.8

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

Available Modules

module load Bracken/2.7-GCC-11.3.0

Nucleotide-resolution analysis of structural variants

Available Modules

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

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

Available Modules

module load CCL/1.12-GCCcore-9.2.0
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-gimkl-2017a

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

Available Modules

module load CDO/2.1.1-gimpi-2022a

module load CDO/2.0.5-GCC-7.1.0
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

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.

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/3.27.7

module load CMake/3.22.1

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

Available Modules

module load CNVnator/0.4-GCC-7.4.0

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

Available Modules

module load CNVpytor/1.3.1-gimkl-2022a-Python-3.11.3

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

Available Modules

module load COMSOL/6.1
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

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

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

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

C++ Thread Pool Library

Available Modules

module load CTPL/0.0.2

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.

Automated testing framework for C.

Available Modules

module load CUnit/2.1-3-GCCcore-9.2.0

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

Available Modules

module load Canu/2.2-GCC-11.3.0

Fast data interchange format and capability-based RPC system.

Available Modules

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

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/7.1.0

Classifier for metagenomic sequences

Available Modules

C++11 serialization library

Available Modules

module load Cereal/1.3.0

An asynchronous message-driven C++ communication library targeted towards tightly coupled, high-performance parallel machines.

Available Modules

module load Charm++/6.8.0-CrayIntel-23.02-19

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

Rapid assessment of genome bin quality using machine learning

Available Modules

module load CheckM2/1.0.1-Miniconda3

Assess the quality of metagenome-assembled viral genomes.

Available Modules

A tool to circularize genome assemblies

Available Modules

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

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-11.3.0

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

Available Modules

module load Clair3/1.0.5-Miniconda3

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

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-gimkl-2020a

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

Available Modules

module load ClustalW2/2.1-gimkl-2017a

Clusters contigs and counts reads from de novo assembled transcriptomes.

Available Modules

module load Corset/1.09-GCC-9.2.0

DNA read coverage and relative abundance calculator focused on metagenomics applications

Available Modules

module load CoverM/0.7.0-GCC-12.3.0

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

Available Modules

module load CppUnit/1.15.1-GCCcore-11.3.0

Toolchain using Cray compiler wrapper, using PrgEnv-cray (PE release: February 2023).

Available Modules

module load CrayCCE/23.02

Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: 23.02).

Available Modules

module load CrayGNU/23.02

Toolchain using Cray compiler wrapper, using PrgEnv-intel (PE release: February 2023 with Intel 19 compiler).

Available Modules

module load CrayIntel/23.02-19

Graphical report explorer report explorer for Scalasca and Score-P

Available Modules

module load CubeGUI/4.4.4-GCCcore-9.2.0

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

Available Modules

module load CubeLib/4.6-GCCcore-9.2.0

Cube high-performance C writer library component.

Available Modules

module load CubeWriter/4.5-GCCcore-9.2.0

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

Available Modules

module load Cufflinks/2.2.1-gimkl-2017a

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/3.9.1

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

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

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-gimkl-2017a
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/1.14.0-GCC-11.3.0

Generally Applicable Atomic-Charge Dependent London Dispersion Correction.

Available Modules

module load DFT-D4/3.5.0-intel-2022a

Sequence aligner for protein and translated DNA searches

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

Available Modules

module load DISCOVARdenovo/52488

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

Available Modules

module load DRAM/1.3.5-Miniconda3

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

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

Available Modules

module load DeePMD-kit/2.1.1

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

Available Modules

module load DeepLabCut/2.3.5

Defines the set of modules loaded by default

Available Modules

module load DefaultModules/
Links

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

Available Modules

module load Delft3D/141732-intel-2022a

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/68819-intel-2020a

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

Available Modules

module load Delly/1.1.3

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

Available Modules

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

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

Available Modules

module load Dsuite/20210718-intel-compilers-2022.0.2

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

Available Modules

module load EDTA/2.1.0

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

Eigenvalue SoLvers for Petaflop-Applications .

Available Modules

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

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

R package for integrated construction of Ecological Niche Models.

Available Modules

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

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

module load ESMF/7.1.0r-intel-2018b

A Python framework for the analysis and visualization of phylogenetic trees

EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.

Available Modules

module load EasyBuild/4.9.0

module load EasyBuild/4.9.0

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

Available Modules

module load Eigen/3.4.0

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/3.12.2-GCCcore-9.2.0

module load Embree/3.2.0-GCC-7.1.0

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

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

Available Modules

module load ExaBayes/1.5.1-gimpi-2020a

Exascale Maximum Likelihood for phylogenetic inference using MPI.

Available Modules

module load ExaML/3.0.22-gimkl-2020a

Tool for estimating repeat sizes

Available Modules

module load ExpansionHunter/5.0.0

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

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

Tools for Short-Reads FASTA/FASTQ files preprocessing.

Available Modules

module load FASTX-Toolkit/0.0.14-gimkl-2017a

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

module load FCM/2019.09.0-GCC-9.2.0
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/6.7.1-CrayIntel-23.02-19

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/3.3.9-CrayIntel-23.02-19

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

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

Available Modules

module load FFmpeg/3.4.2-GCC-7.1.0

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

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

FTGL is a free cross-platform Open Source C++ library that uses Freetype2 to simplify rendering fonts in OpenGL applications. FTGL supports bitmaps, pixmaps, texture maps, outlines, polygon mesh, and extruded polygon rendering modes.

Available Modules

module load FTGL/2.1.3-rc5-GCCcore-7.4.0

module load FTGL/2.1.3-rc5-GCC-7.1.0

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

Available Modules

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

Available Modules

module load FastME/2.1.6.2-GCC-9.2.0

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

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

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

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

Available Modules

module load File-Rename/1.13-GCC-9.2.0

Tool for filtering long reads by quality.

Available Modules

module load Filtlong/0.2.0

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

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

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

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

Available Modules

module load FragGeneScan/1.31-gimkl-2018b

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

FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data.

Available Modules

module load FreeSurfer/7.2.0-centos7_x86_64

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

Available Modules

Free Implementation of the Unicode Bidirectional Algorithm.

Available Modules

module load FriBidi/1.0.12-GCC-12.3.0

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.

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/12.3.0

module load GCC/9.2.0
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/12.3.0

module load GCCcore/9.2.0

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

Genome-wide Efficient Mixed Model Association

Available Modules

module load GEMMA/0.98.4-GCC-9.2.0

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

Available Modules

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

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

Available Modules

module load GLib/2.53.1-GCC-7.1.0

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

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

GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools.

Available Modules

module load GMT/6.4.0-GCC-7.1.0
Links

A genetic algorithm for docking flexible ligands into protein binding sites

Available Modules

module load GOLD/2022
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

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

The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data.

Available Modules

module load GRADS/2.2.0-GCC-7.1.0

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/8.2.1-gimkl-2022a

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

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.

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.

GStreamer plug-ins and elements.

Available Modules

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

GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.

Available Modules

module load GStreamer/1.16.2-GCC-9.2.0

module load GStreamer/1.16.0-GCC-7.1.0

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

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

Available Modules

module load GTK+/3.24.23-GCC-9.2.0

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

module load GTS/0.7.6-CrayGNU-23.02

module load GTS/121130-GCC-7.1.0
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

Available Modules

module load Gaussian/09-D.01
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

Eukaryotic gene prediction suite with automatic training

Available Modules

module load GeneMark-ES/4.71-GCC-11.3.0

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

Available Modules

module load GenoVi/0.2.16-Miniconda3

GenomeThreader is a software tool to compute gene structure predictions.

Available Modules

module load GenomeThreader/1.7.3-Linux_x86_64-64bit

Gerris is a Free Software program for the solution of the partial differential equations describing fluid flow. This module also includes GfsView, a visualisation application for Gerris output.

Available Modules

module load Gerris/20180227-gimkl-2018b

module load Gerris/20180227-gimpi-2018b

Toolkit to assemble organelle genome from genomic skimming data.

Available Modules

module load GetOrganelle/1.7.7.0-gimkl-2022a

Gene finder based on a Generalized Hidden Markov Model.

Available Modules

module load GlimmerHMM/3.0.4-gimkl-2018b

An open source programming language

Available Modules

module load Go/1.21.3

module load Go/1.19.1
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

Genealogies Unbiased By recomBinations In Nucleotide Sequences

Available Modules

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

Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.

Available Modules

module load Guile/1.8.8-GCC-5.4.0

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/4.2.13-iccifort-2018.1.163-GCC-7.1.0-fortran
Links

HDF-EOS (Hierarchical Data Format - Earth Observing System) is a self-describing file format for transfer of various types of data between different machines based upon HDF. HDF-EOS is a standard format to store data collected from EOS satellites: Terra, Aqua and Aura.

Available Modules

module load HDF-EOS/2.19v1.00-GCC-7.1.0

HDF-EOS (Hierarchical Data Format - Earth Observing System) is a self-describing file format for transfer of various types of data between different machines based upon HDF. HDF-EOS is a standard format to store data collected from EOS satellites: Terra, Aqua and Aura.

Available Modules

module load HDF-EOS5/5.1.15-GCC-7.1.0

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

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

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.

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 HMMER2/2.4i-GCC-11.3.0

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

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

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

HarfBuzz is an OpenType text shaping engine.

Available Modules

module load HarfBuzz/4.4.1-GCC-12.3.0

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/20210803

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

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

Available Modules

module load HybPiper/2.0.1rc-Miniconda3

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/2.25.0-gimkl-2022a

ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.

Available Modules

module load ICU/71.1-GCC-11.3.0

module load ICU/62.1-GCC-7.1.0
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-gimkl-2018b

IDL is the trusted scientific programming language used across disciplines to extract meaningful visualizations from complex numerical data.

Available Modules

module load IDL/8.7
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/2.16.1
Links

Genotype imputation and haplotype phasing.

Available Modules

module load IMPUTE/2.3.2

Efficient phylogenomic software by maximum likelihood

Available Modules

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

Intelligent Storage Acceleration Library

Available Modules

ImageMagick is a software suite to create, edit, compose, or convert bitmap images

Available Modules

module load ImageMagick/7.0.9-5-GCCcore-9.2.0

module load ImageMagick/7.0.8-11-GCC-7.1.0

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

Available Modules

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

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

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

Available Modules

A programmer-oriented testing framework for Java.

Available Modules

module load JUnit/4.12

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-GCC-7.1.0

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

Available Modules

module load Java/20.0.2

module load Java/1.8.0_144

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

Available Modules

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

A high-level, high-performance dynamic language for technical computing. This version was compiled from source with USE_INTEL_JITEVENTS=1 to enable profiling with VTune.

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-2020a