Software installed on PSC systems

 This list includes software installed on most PSC computing resources. Anton runs specific software written for its specialized hardware and is not included here.  See the Anton document for specifics on Anton.

The Module package

The environment management package Module is essential for running software on most PSC systems.  Be sure to check if there is a module for the software you want to use by typing module avail software-name

To load the environment for a software package, which defines paths and variables needed to use the software, type module load software-name.

The module help software-name command lists any additional modules that must also be loaded.  Note that in some cases the order in which these additional modules are loaded matters. See documentation on the module command for more information.





Software Description Computing Resource
Abaqus Suite for finite element analysis and computer-aided engineering You must have your own license.
Abinit Calculates electronic density and derived properties of materials (incl. molecules, surfaces & solids) within DFT using pseudopotentials and a planewave or wavelet basis Bridges, Olympus
ABySS Parallel assembler for short read sequence data Bridges, Olympus
AIPS Astronomical Image Processing System Bridges, Olympus
AllPaths-LG Whole-genome shotgun assembler that can generate high-quality genome assemblies using short reads Bridges, Olympus
AMBER Package of molecular simulation programs You must have your own license. PSC can help with installation.
Anaconda Open data science platform, includes popular Python, R and SCALA packages Bridges, Olympus
Annovar Functionally annotates genetic variants detected from diverse genomes Bridges, Olympus
ANSYS General purpose finite element modeling package Bridges, Olympus
Anvi'o Analysis and visualization of 'omics data Bridges, Olympus
ARAGORN Detects tRNA, mtRNA and tmRNA genes Bridges, Olympus
Aspera Allows for rapid transfer of large files and data sets Bridges, Olympus
ATLAS ANSI C and Fortran77 interfaces for the entire BLAS API, and a some of the LAPACK AP Bridges, Olympus
Augustus Predicts genes in eukaryotic genomic sequences Bridges, Olympus
Autodock Predicts how small molecules, e.g., substrates or drug candidates, bind to a receptor of known 3D structure Bridges, Olympus
BAMTools C++ API and toolkit for analyzing and managing BAM files Bridges, Olympus
Barrnap Predicts location of ribosomal RNA genes in genomes Bridges, Olympus
Bazel Open source tool that allows for automation of building and testing of software Bridges, Olympus
BCFTools Utilities for variant calling and manipulating VCFs and BCFs Bridges, Olympus
Bedops Tools to address common questions raised in genomics studies Bridges, Olympus
Bedtools Utilities for comparing, summarizing and intersecting genomic features in the UCSC Genome Browser BED format Bridges, Olympus
BerkeleyGW Calculates the quasiparticle properties and the optical responses of a large variety of materials Bridges, Olympus
Bismark Bisulfite read mapper and methylation caller Bridges, Olympus
BLASR Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement Bridges, Olympus
BLAST Search tool that finds regions of local similarity between nucleotide or protein sequences Bridges, Olympus
BLAT Alignment tool like BLAST, but structured differently Bridges, Olympus
Boost Peer reviewed C++ source libraries Bridges, Olympus
Bowtie Ultrafast, memory-efficient short read aligner. See related tool Bowtie2. Bridges, Olympus
Bowtie2 Ultrafast, memory-efficient tool for aligning sequencing reads to long reference sequences. See related tool Bowtie. Bridges, Olympus
BUSCO Assesses genome assembly and annotation completeness Bridges, Olympus
BWA Fast light-weight tool that aligns relatively short sequences to a sequence database Bridges, Olympus
C, C++ Programming languages Bridges, Olympus
Caffe Deep learning framework Bridges, Olympus
Caffe2 Deep learning framework Bridges, Olympus
Canu Fork of the Celera Assembler designed for high-noise single-molecule sequencing Bridges, Olympus
CDBFASTA FASTA file indexing and retrieval tool Bridges, Olympus
CD-HIT Tool to cluster and compare protein or nucleotide sequences Bridges, Olympus
Celera Assembler De novo WGS DNA sequence assembler Bridges, Olympus
Centrifuge Rapid and efficient classification of DNA sequences from microbial samples Bridges, Olympus
CFITISO Library of C and Fortran routines for reading and writing data in FITS format Bridges, Olympus
CFOUR (Coupled-Cluster techniques for Computational Chemistry), high level quantum chemical calculations Bridges, Olympus
Chainer Powerful, flexible, intuitive framework for neural networks Bridges, Olympus
CHARMM Molecular simulation with broad application to many-particle systems. Comprehensive set of energy functions, enhanced sampling methods, and support for multi-scale techniques Bridges, Olympus
CheckM Tools for assessing genome quality recovered from isolates, single cells or metagenomes Bridges, Olympus
Circos Produces visualizations in a circular layout, commonly used for genomics data Bridges, Olympus
Clustal Omega and Clustal W General purpose fast MSA for protein and RNA/DNA Bridges, Olympus
CMake Tools to control the compilation process, build, test and package software Bridges, Olympus
CNVkit Command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing Bridges, Olympus
CP2K Atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems Bridges, Olympus
CUDA Parallel computing platform and API model  Bridges, Olympus
Cutadapt Reads a FASTA or FASTQ file, finds and removes adapters, writes the changed sequence to standard output Bridges, Olympus
Dammit Simple de novo transcriptome annotator Bridges, Olympus
DDT Debugger for C, C++ and Fortran 90 threaded and parallel codes Bridges, Olympus
deepTools Suite of python tools for the efficient analysis of high-throughput sequencing data Bridges, Olympus
DESMOND High-speed molecular dynamics simulations of biological systems with novel parallel algorithms and numerical techniques for high performance and accuracy Bridges, Olympus
Detonate DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation Bridges, Olympus
DIAMOND Alignment tool for aligning short DNA sequencing reads to a protein reference database Bridges, Olympus
Discovar de novo
Variant caller and small genome assembler
Large (and small) de novo genome assembler
Bridges, Olympus
DReAMM Designs, renders and animates the output from a MCell simulation  
ECTOOLS Long read correction, plus other correction tools Bridges, Olympus
Eigen C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms Bridges, Olympus
ELPH (Estimated Location of Pattern Hits), general purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences Bridges, Olympus
EMBOSS European Molecular Biology Open Software Suite Bridges, Olympus
EricScript Computational framework for the discovery of gene fusions in paired end RNA-seq data. Bridges, Olympus
Exonerate Generic tool for pairwise sequence comparison, allowing sequence alignment using many alignment models Bridges, Olympus
Falcon Collection of genome assembly tools Bridges, Olympus
FASTA-Splitter Divides a single FASTA file into multiple files Bridges, Olympus
FASTQ-Splitter Divides a single FASTQ file into multiple files Bridges, Olympus
FastQC Quality control tool for high throughput sequence data Bridges, Olympus
FASTX Toolkit Command line tools for Short-Reads FASTA/FASTQ files preprocessing Bridges, Olympus
FFmpeg Libraries and programs for handling multimedia data Bridges, Olympus
FFTW3 C subroutine library for computing the DFT in one or more dimensions, of arbitrary input size, of both real and complex data Bridges, Olympus
FLASh Fast and accurate tool to merge paired-end reads from NGS experiments Bridges, Olympus
Fluent Computational fluid dynamics, part of ANSYS Bridges, Olympus
Fortran Programming language Bridges, Olympus
FragGeneScan Finds fragmented genes in short reads and predicts prokaryotic genes in incomplete assemblies or complete genomes Bridges, Olympus
FTOOLS Utility programs to create, examine and modify FITS files Bridges, Olympus
Galaxy Open, web-based platform for data intensive biomedical research.  Bridges, Olympus
GAMESS Ab initio molecular quantum chemistry Bridges, Olympus
Gateway Usage Reporting Monitors, records, and reports on the history of message traffic between API Gateway instances and various services, remote hosts, and clients running in a managed domain Bridges, Olympus
GATK Genome Analysis Toolkit, for high-throughput sequencing data Bridges, Olympus
Gaussian Electronic structure program Bridges, Olympus
GCC (GNU Compiler Collection) Compiler system supporting various programming languages Bridges, Olympus
GDAL Geospatial Data Abstraction Library Bridges, Olympus
GDC client Tools for downloading data from the Genome Data Commons Bridges, Olympus
Genome MuSiC Tools to discover the significance of somatic mutations found in a cohort of cancer samples, and with respect to various external data sources Bridges, Olympus
GFFREAD GFF/GTF parsing utility providing format conversions, region filtering, and FASTA sequence extraction Bridges, Olympus
Gflags Command line flag library Bridges, Olympus
Git Version control system for tracking changes in files and coordinating work on files among multiple people Bridges, Olympus
GlimmerHMM Eukaryotic Gene-Finding System based on a GHMM Bridges, Olympus
Glimmer3 System for finding genes in microbial DNA, especially the genomes of bacteria, archaea and viruses Bridges, Olympus
glog Library which implements application-level logging Bridges, Olympus
GNU Parallel Shell tool for executing jobs in parallel using one or more computers Bridges, Olympus
GPAW Density-functional theory Python code based on the projector-augmented wave method and the atomic simulation environment Bridges, Olympus
Grace WYSIWYG 2D plotting tool for Unix-like operating systems Bridges, Olympus
GraPhlAn Tool for producing high quality circular representations of taxonomic and phylogenetic trees Bridges, Olympus
GROMACS Molecular dynamics software primarily designed for biomolecular systems Bridges, Olympus
Gurobi Mathematical programming solver Bridges, Olympus
Hadoop Big Data processing framework Bridges, Olympus
HDF5/PHDF5 Data model, library, and file format for storing and managing data and its parallel version Bridges, Olympus
HISAT2 Fast, sensitive alignment, mapping NGS reads (DNA & RNA) to a population of human genomes or against a single reference genome Bridges, Olympus
HMMER Biosequence analysis using profile hidden Markov models Bridges, Olympus
Homer Suite of tools for motif discovery and next-gen sequence analysis Bridges, Olympus
HPN-SSH Series of patches for OpenSSH to provide improved performance and functionality Bridges, Olympus
HTSeq Analysis of high-throughput sequencing data using Python Bridges, Olympus
HUMAnN2 Pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomatic sequencing data  Bridges, Olympus
ICC Intel compilers, libraries and MPI implementation Bridges, Olympus
IDBA-TRAN Iterative De Bruijn Graph De Novo Assembler short read assembler for transcriptomes Bridges, Olympus
IDBA-UD Iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth Bridges, Olympus
Infernal Searches DNA sequence databases for RNA structure and sequence similarities Bridges, Olympus
Java Programming language Bridges, Olympus
JAGS Statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo. Bridges, Olympus
Jellyfish/Jellyfish2 Tool for fast, memory efficient counting of k-mers in DNA Bridges, Olympus
JPEG Method of lossy compression for digital images Bridges, Olympus
Julia High-level, high-performance dynamic programming language for numerical computing Bridges, Olympus
Jupyter Create and share code, visualizations, equations, more Bridges, Olympus
kallisto Quantifies abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads Bridges, Olympus
Keras Minimalist, highly modular neural networks library written in Python and capable of running on top of either TensorFlow or Theano Bridges, Olympus
khmer Tools to work with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells Bridges, Olympus
Kraken System for assigning taxonomic labels to short DNA sequences Bridges, Olympus
LAMMPS Classical molecular dynamics code Bridges, Olympus
Lasagne Lightweight library to build and train neural networks Bridges, Olympus
LevelDB Fast key-value storage library that provides an ordered mapping from string keys to string values. Bridges, Olympus
LSMS Locally Self-consistent Multiple Scattering method, an order-N approach to the calculating the electronic structure of large systems within the local density approximation  
MACS Model-based Analysis of ChIP-Seq, for identifying transcript factor binding sites Bridges, Olympus
MACSE Aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons Bridges, Olympus
MAFFT Multiple sequence alignment program Bridges, Olympus
Magma Dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, e.g., multicore+GPU systems Bridges, Olympus
MAKER Genome annotation pipeline Bridges, Olympus
MALLET NLP, document classification and other machine learning applications for text Bridges, Olympus
MALT MEGAN Alignment Tool, an extension of MEGAN Bridges, Olympus
MAP Profiles C, C++ and Fortan applications Bridges, Olympus
Mapsembler2 Targeted assembly software Bridges, Olympus
MARVEL Tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads Bridges, Olympus
MaSuRCA Whole genome assembly, combining the efficiency of the de Bruijn graph and Overlap-Layout-Consensus approaches Bridges, Olympus
Mathematica Mathematical symbolic computation program Bridges, Olympus
MATLAB High-level language and interactive environment, performs computationally intensive tasks faster than traditional languages Bridges, Olympus
Maven Apache build manager for Java projects Bridges, Olympus
MAXBIN Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm Bridges, Olympus
MCell Monte Carlo Cell, simulates the movements and reactions of molecules within and between cells  
MCT Model Coupling Toolkit, fully parallel library for creating coupled models Bridges, Olympus
MEGAHIT A single node assembler for large and complex metagenomics NGS reads, such as soil Bridges, Olympus
MEGAN MEta Genome ANalyzer Bridges, Olympus
Meraculous Whole genome assembler for Next Generation Sequencing data geared for large genomes Bridges, Olympus
MetaPhlAn/ MetaPhlAn 2 Computational tools for profiling the composition of microbial communities from metagenomic shotgun sequencing data Bridges, Olympus
MetaVelvet Extension of Velvet assembler to de novo metagenome assembly from short sequence reads Bridges, Olympus
Methylpy Bisulfate sequencing data processing and differential methylation analysis Bridges, Olympus
Metis Serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices Bridges, Olympus
MinCED Program to find CRISPRs in full genomes or environmental datasets such as metagenomes Bridges, Olympus
MIRA Whole genome shotgun nd EST sequence assembler Bridges, Olympus
MKL Math Kernel Library, highly optimized and threaded routines for linear algebra, FFTs, vector math and random number generators Bridges, Olympus
Mothur Tool to analyze microbial communities Bridges, Olympus
MPI Message Passing Interface. Both Intel MPI and Open MPI are available. Bridges, Olympus
MPI-Caffe Combines MPI and Caffe to enable simple, modular design of deep networks that span multiple machines Bridges, Olympus
Mrjob Python package that helps write and run Hadoop Streaming jobs Bridges, Olympus
MUMmer System for rapidly aligning entire genomes, whether in complete or draft form Bridges, Olympus
MUSCLE General purpose fast MSA Bridges, Olympus
MVAPICH Library exploiting novel features and mechanisms of high-performance networking technologies. Delivers improved performance and scalability to MPI applications. Bridges, Olympus
MyCC Automated binning tool that visualizes metagenomes and and identifies reconstructed genomic fragments Bridges, Olympus
NAMD Parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems Bridges, Olympus
NCL Graphics NCAR Command Language graphics library Bridges, Olympus
NetCDF Software libraries and self-describing, machine-independent data formats supporting the creation, access, and sharing of array-oriented scientific data Bridges, Olympus
NEURON Simulation environment for modeling individual neurons and networks of neurons Bridges, Olympus
NGSCheckMate Identifies NGS data files from the same individual Bridges, Olympus
NWCHEM Computes the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density Bridges, Olympus
OnDemand Web browser interface to manage files, submit and track jobs on Briges Bridges, Olympus
OpenBLAS Optimized BLAS library Bridges, Olympus
OpenCV Open source library of several hundred computer vision algorithms Bridges, Olympus
OpenFOAM Finite volume CFD package Bridges, Olympus
OpenMPI High performance message passing library Bridges, Olympus
OpenSlide Library that provides simple interface to read whole-slide images Bridges, Olympus
PAML Phylogenetic analyses of DNA or protein sequences using maximum likelihood Bridges, Olympus
PANDOC Universal document converter Bridges, Olympus
PAPI Performance API, specifies a API for accessing hardware performance counters Bridges, Olympus
Parmetis MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices Bridges, Olympus
ParselTongue Python interface to classic AIPS, Obit, and other task-based data reduction packages Bridges, Olympus
PBJELLY Highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles Bridges, Olympus
Perl Programming language Bridges, Olympus
PETSc Suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations Bridges, Olympus
PGI PGI compilers and Tools Bridges, Olympus
PHYLIP Package for inferring phylogenies Bridges, Olympus
Phylosift Tool suite to conduct phylogenetic analysis of genomes and metagenomes Bridges, Olympus
Picard Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files Bridges, Olympus
Pilon Automatically improves draft assemblies and finds variation among strains, including large event detection Bridges, Olympus
Platanus De novo sequence assembler for NGS data Bridges, Olympus
PLINK/SEQ Open-source C/C++ library for working with human genetic variation data Bridges, Olympus
PLUMED Performs free energy calculations in molecular systems Bridges, Olympus
PNG Raster graphics file format that supports lossless data compression Bridges, Olympus
Pplacer Places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment Bridges, Olympus
Primer3 Designs PCR (Polymerase Chain Reaction) primers; can also design hybridization probes and sequencing primers Bridges, Olympus
ProbCons Generates multiple alignments of protein sequences usinprobabilistic modeling and consistency-based alignment techniques Bridges, Olympus
Prodigal Open source lightweight microbial genefinding program Bridges, Olympus
Prokka Software tool for rapid annotation of prokaryotic genomes Bridges, Olympus
Protocol buffer Protocol Buffers, method of serializing structured data Bridges, Olympus
Psi4 Open source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties Bridges, Olympus
Python (including  matplotlib, numpy, scipy) Powerful, object-oriented programming language Bridges, Olympus
PyTorch Flexible and intuitive deep-learning framework Bridges, Olympus
Qt Cross-platform application development framework Bridges, Olympus
QoRTS Fast, efficient, portable multifunction toolkit to for analysis, quality control, data management of RNA-Seq datasets Bridges, Olympus
Quantum Espresso Integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale Bridges, Olympus
R, RStudio (including the ggplot2 package) Language and environment and an IDE for statistical computing and graphs Bridges, Olympus
RAxML Maximum likelihood phylogeny estimation for interpreting relationships between sets of data Bridges, Olympus
Ray Parallel de novo genome assembly using MPI Bridges, Olympus
Relion An empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy Bridges, Olympus
Repeatmasker Screens DNA sequences for interspersed repeats and low complexity DNA sequences Bridges, Olympus
RNAmmer Predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences Bridges, Olympus
Rosetta Software suite including algorithms for computational modeling and analysis of protein structures Bridges, Olympus
RSEM Estimates gene and isoform expression levels from RNA-Seq data Bridges, Olympus
Sailfish Alignment-free isoform quantification from RNA-seq reads using lightweight algorithms Bridges, Olympus
Salmon Tool for fast transcript quantification from RNA-seq data Bridges, Olympus
SAMtools Utilities for manipulating alignments in SAM format Bridges, Olympus
Scikit-learn Simple and efficient tools for data mining and data analysis, built on NumPy, SciPy and matplotlib Bridges, Olympus
Score Conservation Predicts functionally important residues deom sequence conservation within a multiple sequence alignment Bridges, Olympus
SCOTCH Package and libraries for sequential and parallel graph partitioning, static mapping and clustering, sequential mesh and hypergraph partitioning, and sequential and parallel sparse matrix block ordering Bridges, Olympus
Scythe Adapter/contaminant removal tool for FASTQ files Bridges, Olympus
Seqtk Toolkit for processing sequences in FASTA/Q formats Bridges, Olympus
Shannon Assembles transcripts from RNA-Seq data using an information-theoretic approach Bridges, Olympus
Sickle Windowed adaptive trimming tool for FASTQ files Bridges, Olympus
SIESTA Performs efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids Bridges, Olympus
SignalP Predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes and eukaryotes Bridges, Olympus
Singular Computer algebra system for polynomial computations, includes a C-like programming language Bridges, Olympus
Singularity Open-source software container platform Bridges, Olympus
SNVMIX Detects single nucleotide variants from next generation sequencing data Bridges, Olympus
SOAPdenovo2 De novo assembler for next generation sequencing reads Bridges, Olympus
SomaticSniper Program to identify single nucleotide positions which differ between tumor and normal cells Bridges, Olympus
SPAdes St. Petersburg genome assembler - an assembly toolkit with various assembly pipelines Bridges, Olympus
Spark Open source software web application framework and domain-specific language written in Java Bridges, Olympus
SPRNG Scalable Parallel Random Number Generators library Bridges, Olympus
SRA toolkit Collection of tools and libraries for using data in the INSDC Sequence Read Archives Bridges, Olympus
STAR-Fusion Uses the STAR aligner to dentify candidate fusion transcripts supported by Illumina reads, maps junction and spanning reads to a reference annotation set Bridges, Olympus
STAR Aligner Spliced Transcripts Alignment to Reference, an alignment tool for RNA sequences Bridges, Olympus
Strelka Somatic variant calling workflow for matched tumor-normal samples Bridges, Olympus
StringTie Fast and highly efficient assembler of RNA sequence alignments into potential transcripts Bridges, Olympus
Subread Software suite for processing next-gen sequencing read data Bridges, Olympus
SUNDIALS SUite of Nonlinear and DIfferential/ALgebraic equation Solvers Bridges, Olympus
Super-Deduper Application designed to remove duplicates introduced by PCR amplification Bridges, Olympus
SuperLU Library for the direct solution of large, sparse, nonsymmetric systems of linear equations Bridges, Olympus
Supernova Generates highly-contiguous, phased, whole-genome de novo assemblies from a Chromium-prepared library Bridges, Olympus
SWIG Tool that connects programs written in C and C++ with a variety of other languages, including Python, Java and R. Bridges, Olympus
Szip Fast, cross-platform data compression program Bridges, Olympus
TAU Tuning and Analysis Utilities Bridges, Olympus
TensorFlow Machine learning library for numerical computation using data flow graphs Bridges, Olympus
Theano Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently Bridges, Olympus
TIFF Tagged Image File Format, computer file format for storing raster graphics images Bridges, Olympus
TMHMM Predicts transmembrane helices in proteins Bridges, Olympus
tmux Terminal multiplexer; create and control multiple terminals Bridges, Olympus
TopHat Fast splice junction mapper for RNA-Seq reads Bridges, Olympus
Torch Open source machine learning library, scientific computing network, and script language based on Lua Bridges, Olympus
Trans-ABySS De novo assembly of RNAseq data using ABySS Bridges, Olympus
TransDecoder Identifies candidate coding regions within transcript sequences Bridges, Olympus
Transrate Software for de-novo transcriptome assembly quality analysis Bridges, Olympus
Trilinos Collection of libraries to be used in the development of scientific applications Bridges, Olympus
TrimAl Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment Bridges, Olympus
Trim Galore! A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files Bridges, Olympus
Trinity Package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data Bridges, Olympus
Trinotate Annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms Bridges, Olympus
tRNAscan-se Program for improved detection of transfer RNA genes in genomic sequence Bridges, Olympus
UFRaw Utility to read and manipulate raw images from digital cameras Bridges, Olympus
UNCeqR Method and associated software for discovering somatic mutations using the integration of DNA and RNA sequencing Bridges, Olympus
VarScan Detects variants in NGS data Bridges, Olympus
VASP Atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. You must have your own license. PSC can help with installation.
VCF2MAF Converts a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms Bridges, Olympus
VCFtools Tool providing easily accessible methods for working with complex genetic variation data in the form of VCF files Bridges, Olympus
Velvet De novo genomic assembler specially designed for short read sequencing technologies Bridges, Olympus
VisIt Interactive and scalable visualization, animation and analysis tool Bridges, Olympus
VMD Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting Bridges, Olympus
VTune Performance analysis tool for serial, multithreaded or MPI applications Bridges, Olympus
Weaver Allele-specific quantification of structural variations in cancer genomes Bridges, Olympus
WESTPA Constructs and runs stochastic simulations using the “weighted ensemble” approach of Huber and Kim Bridges, Olympus
WGS See Celera assembler Bridges, Olympus
WIEN2k Electronic structure calculations of solids using DFT You must have your own license. PSC can help with installation.
Xfig and transfig Interactive drawing tools Bridges, Olympus
XHMM Uses principal component analysis (PCA) normalization and a hidden Markov model (HMM) to detect and genotype copy number variation (CNV) from normalized read-depth data from targeted sequencing experiments Bridges, Olympus
Xpdf Open source PDF viewer for X Window System and Motif Bridges, Olympus
Zlib Data compression library Bridges, Olympus
Zoltan Data management services for unstructured, adaptive and dynamic applications Bridges, Olympus

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