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List of modules available on ACCRE

If you cannot find a package you would like to use below, please open a helpdesk ticket with us and we can either help you install it into your home directory, or possibly install it for cluster-wide access.

Last updated December 3, 2018
ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.
ABySS2.0.2Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
AFNI17.2.04AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
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.
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.
ANTs2.2.0ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.
Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
Aspera-CLI3.7.7IBM 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.
AUGUSTUS3.2.3AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
BamTools2.4.0BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
BEDTools2.26.0The 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.
BerkeleyGW2.0.0The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.
biomart-perl0.7_e6db561The BioMart Perl API allows you to go a step further with BioMart and integrate BioMart Perl Code into custom Perl scripts.
BioPerl1.7.1Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.
Biopython1.68 (Py2.7.12)
1.68 (Py3.5.2)
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
Boost1.63.0 (Py2.7.12)
1.63.0 (Py3.5.2)
1.65.1 (Py2.7.14)
1.65.1 (Py3.6.3)
Boost provides free peer-reviewed portable C++ source libraries.
Bowtie22.3.2Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
charmm42b1CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems.
Circos0.69-5Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
CLAPACK3.2.1C version of LAPACK
CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
cutadapt1.9.1 (Py2.7.12)
1.9.1 (Py3.5.2)
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
DBG2OLC20170208DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies
Exonerate2.4.0Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
FFmpeg3.3.1A complete, cross-platform solution to record, convert and stream audio and video.
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.
FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging.
FSL5.0.10FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
FSLeyes0.15.0FSLeyes is the FSL image viewer.
GATE8.0GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography
GATK3.8-0The 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.
Gaussian16.B.01Gaussian provides state-of-the-art capabilities for electronic structure modeling.
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,...).
2.2.3 (Py2.7.14)
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 commandline utilities for data translation and processing.
GDB7.11.1The GNU Project Debugger
Geant410.04Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
gnuplot5.0.5Portable interactive, function plotting utility
grace5.1.25Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.
GraphicsMagick1.3.25GraphicsMagick is the swiss army knife of image processing.
Graphviz2.38.0 (Py2.7.12)
2.40.1 (Py2.7.14)
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.
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.
h5py2.6.0 (Py2.7.12)
2.6.0 (Py3.5.2)
2.7.1 (Py2.7.14)
HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.
Hadoop2.7.7The Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models.
Harminv1.4.1Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.
HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
HISAT22.0.4HISAT2 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).
HTSeq0.9.1 (Py2.7.12)A framework to process and analyze data from high-throughput sequencing (HTS) assays
ImageMagick7.0.5-10ImageMagick is a software suite to create, edit, compose, or convert bitmap images
IMPUTE22.3.2IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009
Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL
Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.
The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.
Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability.
JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
lftp4.7.7LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind.
libctl4.1.4libctl is a free Guile-based library implementing flexible control files for scientific simulations.
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.
MACS22.1.1.20160309 (Py2.7.12)Model Based Analysis for ChIP-Seq data
MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.
matplotlib1.5.3 (Py2.7.12)
1.5.3 (Py3.5.2)
2.1.0 (Py2.7.14)
2.1.0 (Py3.6.3)
matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.
MCRR2016aThe MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.
MEME4.12.0The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.
METIS5.1.0METIS 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.
Mono4.6.2.7An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
MPB1.7.0MPB is a free and open-source software package for computing electromagnetic band structures and modes.
mpi4py1.3.1 (Py2.7.12)
1.3.1 (Py2.7.14)
1.3.1 (Py3.5.2)
1.3.1 (Py3.6.3)
MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.
MRIcron1.0.20180614MRIcron allows viewing of medical images. It includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering.
MultiQC1.2 (Py2.7.14)
1.2 (Py3.6.3)
Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
MUSCLE3.8.31MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line options are needed to perform common alignment tasks.
MySQL is one of the world's most widely used open-source relational database management system (RDBMS).
NAMD2.12NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NiBabel2.1.0 (Py2.7.12)NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.
numpy1.11.1 (Py2.7.12)
1.11.1 (Py3.5.2)
1.13.1 (Py2.7.14)
1.13.1 (Py3.6.3)
NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.
Octave4.2.1GNU Octave is a high-level interpreted language, primarily intended for numerical computations.
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
OpenCV3.1.0OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products.
The Open MPI Project is an open source MPI-2 implementation.
PAML4.9hPAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
pandas0.18.1 (Py2.7.12)
0.18.1 (Py2.7.14)
0.18.1 (Py3.5.2)
0.18.1 (Py3.6.3)
pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.
PANDAseq2.10PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
ParaView5.3.0ParaView is a scientific parallel visualizer.
ParMETIS4.0.3ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.
PEAR0.9.10PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.
Larry Wall's Practical Extraction and Report Language
PHAST1.4PHAST is a freely available software package for comparative and evolutionary genomics.
PheWAS0.12Provides an accessible R interface to the phenome wide association study.
PHYLIP3.696PHYLIP is a free package of programs for inferring phylogenies.
picard2.17.10A set of tools (in Java) for working with next generation sequencing data in the BAM format.
plink-1.9-x86_64: Whole-genome association analysis toolset
PLINKSEQ0.10PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
PostgreSQL9.6.2 (Py2.7.12)
10.3 (Py2.7.14)
PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.
POV-Ray3.7.0.0The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports.
Pysam0.10.0 (Py2.7.12)Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
Python is a programming language that lets you work more quickly and integrate your systems more effectively.
Qhull2015.2Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull.
qrupdate1.1.2qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.
QuantumESPRESSO5.4.0Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
R is a free software environment for statistical computing and graphics.
R-bundle-Bioconductor3.3R is a free software environment for statistical computing and graphics.
RAxML8.2.10RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
RELION2.0.3RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).
ROOT6.10.02 (Py2.7.12)The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way.
RSEM1.3.0RNA-Seq by Expectation-Maximization
Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
ScaLAPACK2.0.2The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
scipy0.17.0 (Py2.7.12)
0.17.0 (Py3.5.2)
0.19.1 (Py2.7.14)
0.19.1 (Py3.6.3)
SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python.
SNPhylo20160204SNPhylo: a pipeline to generate a phylogenetic tree from huge SNP data
SOAPdenovo2r240SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo.
Spark2.2.1Spark is Hadoop MapReduce done in memory
SQLite: SQL Database Engine in a C Library
SRA-Toolkit2.8.2-1The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format
STAR2.5.2bSTAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
Stata14Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics.
Subversion is an open source version control system.
SuiteSparse is a collection of libraries manipulate sparse matrices.
3.0.12 (Py2.7.14)
SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
tabix0.2.6Generic indexer for TAB-delimited genome position files
Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.
Valgrind3.12.0Valgrind: Debugging and profiling tools
VCFtools0.1.14A set of tools written in Perl and C++ for working with VCF files.