Software Installed on PSC Systems

Advancing state of the art high-performance computing, communications and data analytics.

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
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
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
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
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
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
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
BLAT Alignment tool like BLAST, but structured differently Bridges
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
BUSCO Assesses genome assembly and annotation completeness Bridges
BWA Fast light-weight tool that aligns relatively short sequences to a sequence database Bridges
C, C++ Programming languages Bridges
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
Cutadapt Reads a FASTA or FASTQ file, finds and removes adapters, writes the changed sequence to standard output Bridges
Dammit Simple de novo transcriptome annotator Bridges
DDT Debugger for C, C++ and Fortran 90 threaded and parallel codes Bridges
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
FASTX Toolkit Command line tools for Short-Reads FASTA/FASTQ files preprocessing Bridges
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
FLASh Fast and accurate tool to merge paired-end reads from NGS experiments Bridges
Fluent Computational fluid dynamics, part of ANSYS Bridges
Fortran Programming language Bridges
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
Gaussian Electronic structure program Bridges
GCC (GNU Compiler Collection) Compiler system supporting various programming languages Bridges
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
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
HISAT2 Fast, sensitive alignment, mapping NGS reads (DNA & RNA) to a population of human genomes or against a single reference genome Bridges
HMMER Biosequence analysis using profile hidden Markov models Bridges
Homer Suite of tools for motif discovery and next-gen sequence analysis Bridges
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 Intel compilers, libraries and MPI implementation Bridges
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
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
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
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
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
NCL Graphics NCAR Command Language graphics library Bridges
NetCDF 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
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
OpenFOAM Finite volume CFD package Bridges
OpenMPI High performance message passing library Bridges
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 PGI compilers and Tools Bridges
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
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
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
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
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
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
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
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
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
STAR Aligner Spliced Transcripts Alignment to Reference, an alignment tool for RNA sequences Bridges
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
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
Velvet De novo genomic assembler specially designed for short read sequencing technologies Bridges
Interactive and scalable visualization, animation and analysis tool Bridges
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

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.

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