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

Allocations questions
Please see the Allocations FAQ page.
For questions not answered in the FAQ, contact the PSC Allocations department at:
Email: grants@psc.edu
Phone: 412/ 268-4960
Fax: 412/ 268-5831
Introducing Bridges-2
Bridges-2, PSC's newest supercomputer, will debut in early 2021. It will be funded by a $10-million grant from the National Science Foundation.