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Many popular software packages are installed and available as modules.  Frequently, different versions are available and you can use an older version if you specify the version.  The default in most cases is the latest version.  For example, "module load irods" will provide iRods version 3.3, whereas "module load irods/3.0" will make the older version available.

You may request that applications be installed if they have general usefulness like Blast - https://it.arizona.edu/hpc-software-install-request

Ocelote is built on CentOS 6 which is the foundation for all compilers, libraries, and applications.  Some workloads need CentOS 7 for its newer kernel.  A number of GPU nodes have been reprovisioned with a CentOS 7 image. PBS information

There are less applications available on ElGato because the general policy for ElGato is that users will compile or install the applications they need in their home space.

Puma will be available soon.  It is built on CentOS 7.  Many of the same modules will be available and are likely to be newer versions.  There are a couple of important points:
1.  Many utilities and tools are integrated in the operating system and are not modules like on Ocelote.  These are marked with ** and include Singularity, Boost, Curl and FFTW.
2. Due to the naming scheme of our provisioning tool, the default compiler is GCC 8.3, and is called gnu8.  It is 
loaded by default along with the default MPI, which is called openmpi3

Installed Software   

  • The list here is usually incomplete because of the frequent changes.
  • Some modules are in the operating system also, but are too downlevel, like curl or libtool.
  • The current list of modules is available on each login node with the command "module avail".
  • Module commands are available here.
  • Puma is likely to have a newer version of the same software.
  • Puma** or Ocelote** indicates software that is installed to the operating system and not a module. 
SoftwareDescription

Computing
Resource 

AbaqusFinite element analysisOcelote 
Puma
Abyss

Parallel assembler for short read sequence data

Ocelote 
Puma
Allpaths-LGShort read genome assemblerOcelote
AnacondaPlatform for data science and machine learningOcelote
Puma
AnsysLicensed:

General purpose finite element modeling package

Ocelote 
Puma
Ant

JAVA build tool

Ocelote 
Puma
AOCLAMD Optimized CPU Libraries. Includes BLIS, libFLAME, FFTW, LibM, ScaLAPACKPuma
AugustusGene prediction and is required for MakerOcelote 
Puma
AutoconfGNU tool for producing configure scripts for building, installing and packaging software on computer systems where a Bourne shell is availableOcelote
Puma**
Bamtools

C++ API and toolkit for analyzing and managing BAM files

Ocelote 
Puma
BbmapShort read aligner for DNA and RNA-seq dataOcelote
Puma
BcftoolsA set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCFOcelote
Puma
Beagle-libPhylogenetics - works with BeastOcelote
Puma
BeastBayesian analysis of molecular sequences Ocelote
Puma
Bedtools

Utilities for comparing, summarizing and intersecting genomic features in the UCSC Genome Browser BED format

Ocelote 
Puma
BiocontainersBiocontainers is a registry of Biology tools that can pulled from a Docker container into a Singularity container.Ocelote
Blas

Basic Linear Algebra Subprograms

Ocelote**
Elgato 
Puma**
Blast

Search tool that finds regions of local similarity between nucleotide or protein sequences

Ocelote 
Puma**
BlatAlignment tool like BLAST, but structured differentlyOcelote
Puma
Blender3D Visualization softwarePuma
Boost

Peer reviewed C++ source libraries

Ocelote**
Puma**
Bowtie

Ultrafast, memory-efficient short read aligner. See related tool Bowtie2

Ocelote 
Bowtie2

Ultrafast, memory-efficient tool for aligning sequencing reads to long reference sequences. See related tool Bowtie

Ocelote 
Puma
BWA

Fast light-weight tool that aligns relatively short sequences to a sequence database

Ocelote
Puma 
Bzip2Compresses data in blocks of size between 100 and 900 kB and uses the Burrows–Wheeler transform to convert frequently-recurring character sequences into strings of identical lettersOcelote
Puma**
Canu

Fork of the Celera Assembler designed for high-noise single-molecule sequencing

Ocelote 
CentrifugeSource code that is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samplesOcelote
Cern-RootA modular scientific software frameworkOcelote
Puma**
CfitsioA library of subroutines for data filesOcelote
Puma**
Chapel

Programming language designed for productive parallel computing at scale

Ocelote 
ClusterThe open source clustering software implements the most commonly used clustering methods for gene expression data analysisOcelote
Cmake

Tools to control the compilation process, build, test and package software; invoke via the On Ocelote use the "cmake3" command for cmake 3.x CMakefiles, in place of the Elgato only method of "module load cmake;cmake".

Ocelote**
Elgato
Puma 

ComsolModeling and simulating physics-based problems (licensed)Ocelote
Puma
ContribAdds user supported software to your module path. On Ocelote this is /unsupportedPuma
CplexIBM optimization models, combining leading solver engines with a tightly integrated IDE and modeling languageOcelote 
Cuda

Parallel computing platform and API model for Nvidia GPU's

Elgato
Ocelote
Puma

Cufflinks

Assembles transcripts, estimates their abundances, tests for differential expression and regulation in RNA-Seq samples

Ocelote 
Puma
CurlComputer software project providing a library and command-line tool for transferring data using various protocolsOcelote
Puma**

dbg2olc

Efficient assembly of large genomesOcelote
Diamond

Alignment tool for aligning short DNA sequencing reads to a protein reference database

Ocelote
dDocentQuality filtering using TrimmomaticOcelote
Ea-utils

Command-line tools for processing biological sequencing data

Ocelote 
Eigenhigh-level C++ library of template headersOcelote
Exonerate

Generic tool for sequence comparison

Ocelote 
Puma
FastmeAlgorithms to infer phylogeniesOcelote
Puma
FastQC

Quality control tool for high throughput sequence data

Ocelote 
Puma
FastQTLQTL mapping softwareOcelote
FasttreeFor large alignmentsOcelote
Puma
FastX

Command line tools for Short-Reads FASTA/FASTQ files preprocessing

Ocelote 
Puma
FFmpegA cross-platform solution to record, convert and stream audio and videoOcelote
Puma
FFTWFast fourier transforms. Ocelote has multiple versions

ElGato
Ocelote
Puma** 

FragGeneScan

Finds fragmented genes in short reads and predicts prokaryotic genes

Ocelote 
FreeBayesBayesian genetic variant detector designed to find small polymorphismsOcelote
Puma
FreecQuantifying transcriptsOcelote
FreesurferAnalysis of neuroimaging dataOcelote
GATKIdentifying SNPs and indels in germline DNA from Broad InstituteOcelote
Gaussian

Electronic structure program. Licensed for general use

Ocelote 
Puma
GDALa computer software library for reading and writing raster and vector geospatial data formatsOcelote
Puma**
GEOSGeometry Engine Open SourceOcelote
Puma**
GitVersion control system (VCS) for tracking changes in computer files and coordinating work on those files among multiple people.Ocelote
Puma**
GmapCross platform, open source .NET controlOcelote
Gnuplot

Generates two- and three-dimensional plots of functions

Ocelote**

GoProgramming language from GoogleOcelote
Puma
GossamerBioinformatics suiteOcelote
Graphviz

Open source graph visualization software (included in Anaconda also)

Ocelote**
Gromacs

Molecular dynamics software primarily designed for biomolecular systems

Ocelote
Puma
GSL

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers

ElGato
Ocelote 
Puma
GurobiMathematical problem solver for prescriptive analyticsOcelote
HDF5

Data model, library, and file format for storing and managing data

ElGato
Ocelote
Puma
HISAT2A fast and sensitive alignment program for mapping next-generation sequencing reads.
Replaces TopHat
Puma
HMMER

Biosequence analysis using profile hidden Markov models

Ocelote 
Puma
hpctoolkitTools for measurement and analysis of program performancePuma
htslibUnified C library for accessing common file formats. Also part of samtoolsOcelote
Puma
hwlocGathers information about parallel computing platforms so as to exploit them efficiently Ocelote
Puma
HYPRELibrary of linear solvers featuring parallel multigridOcelote
Puma
IDL

Restricted: Interactive Data Language, is a programming language used for data analysis, particularly in astronomy

ElGato
Ocelote 
Puma

Intel CompilersLicensed compilers

ElGato
Ocelote
Puma 
Intel MPIIntel MPI (integrated from 2019 on)Ocelote 
Puma
Intel ToolkitIntel DAAL, GDB, IPP, MKL, TBB, Intel-Cluster (integrated from 2019 on)Ocelote
Puma
IQ-TREEEfficient phylogenetic software Ocelote
iRodsClient - open source data managementOcelote **
Puma **
JagsAnalysis of Bayesian hierarchical models using Markov Chain Monte Carlo simulationOcelote
JavaProgramming languageOcelote 
Puma**
JellyfishFast, memory-efficient counting of k-mers in DNA. Used by TrinityOcelote
Puma
Julia

High-level, high-performance dynamic programming language for technical computing

Ocelote
Puma
JupyterJupyter notebooks are available at the web service OnDemandOcelote
Elgato
Puma
KallistoQuantifying abundances of transcripts from RNA-Seq dataOcelote
Puma
Lammps

Classical molecular dynamics code

Ocelote 
Puma
LapackNumerical linear algebraElGato
Ocelote 
Puma**
LibtoolGeneric library building toolOcelote
Puma**
LS-OPT (lsopt)Design optimizationOcelote
Puma
MAFFT

Multiple sequence alignment program

Ocelote 
Puma
Maker

Portable and easily configurable genome annotation pipeline

Ocelote
Puma 
MathematicaLicensed: A single integrated, continually expanding system that covers the breadth and depth of technical computingOcelote 
Puma
MATLAB

High-level language and interactive environment, performs computationally intensive tasks

ElGato
Ocelote 
Puma
MavenA build automation tool used primarily for Java projectsOcelote
Puma
MCLA cluster algorithm for graphsOcelote
Puma
MemeSuite of motif-based sequence analysis toolsOcelote
Puma
MetaPhlAnA computational tool for profiling the composition of microbial communitiesOcelote
MigrateSoftware that estimates population parameters, effective population sizes and migration rates of n populations, using genetic dataOcelote
MooseAn open-source parallel finite element frameworkOcelote
MothurSoftware for microbial biologyOcelote
Puma
MrbayesProvides bayesian estimation of phylogenyOcelote
MPICH/2

Freely available, portable implementation of MPI. Renamed to MPICH

Ocelote 
Puma
MVAPICH

Library exploiting novel features and mechanisms of high-performance networking technologies

Ocelote
MummerRapid whole genome alignmentOcelote
NAMDMolecular dynamics. Cuda version is "namd-cuda"Ocelote
NCL (ncl-ncarg)NCAR Command LanguageOcelote
Puma
NCOToolkit to manipulate and analyze data stored in netCDF formatOcelote
Puma
NetCDF

Software libraries and self-describing, machine-independent data formats supporting the creation, access, and sharing of array-oriented scientific data

Ocelote 
Puma
NetlogoA programmable modeling environment for simulating natural and social phenomenaOcelote
Puma
NGS-SDK

A new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.
Works with HISAT2 and SRAToolkit

Puma
OpenblasAn optimized BLAS libraryOcelote
Puma
OpenFOAMComputational Fluid Dynamics softwareOcelote
Puma
OpenMPI

High performance message passing library

ElGato
Ocelote 
Puma
OrthoFinder

Accurate inference of orthogroups, orthologues, gene trees and rooted species

Ocelote 
Puma
PandaseqA program to align illumina readsOcelote
PapiPerformance application programming interfacePuma
ParallelGNU Parallel is a shell tool for executing jobs in parallelOcelote
Puma
Paraview

ParaView is an open-source, multi-platform data analysis and visualization application.
Client-server headless version is installed on ElGato and Puma

ElGato 
Ocelote
Puma
ParflowA parallel integrated hydrology modelOcelote
ParMETISAn MPI-based parallel library
Integrated in PetSc on Puma
Ocelote
Puma
Pasta

Practical Alignment using Sate and TrAnsitivity. This is installed to python/2.
module load python/2. Then pip list will display available modules 

Ocelote
PCREA set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.Ocelote
Puma**
PeridigmComputational peridynamics code from Sandia NLOcelote
PerlProgramming language

Ocelote 
Puma**

PETScA suite of data structures and routines developed by Argonne National Laboratory for the scalable (parallel) solution of scientific applications modeled by partial differential equations.  The default version is built with GCC and real arithmetic.  There are other modules built with Intel compilers and complex arithmetic support.Ocelote
Puma
PGIPGI Compilers and ToolsOcelote
Photoscan-proPerforms photogrammetric processing of digital images and generates 3d spatial dataOcelote
PicardCommand line tools for manipulating high-throughput sequencingOcelote
Puma
Plink

Whole genome association analysis toolset

Ocelote
Puma
ProjCartographic projections and coordinate transformations libraryOcelote
Proj
PythonObject-oriented programming language
We encourage the use of virtualenv to build your own environment.
ElGato
Ocelote 
Puma
QctoolSoftware to filter out samples or variantsOcelote
Qiime

Quantitative Insights Into Microbial Ecology. Qiime2 is a package in Python3

Ocelote
Quantum-espressoMaterials modellingOcelote
R

Language and environment for statistical computing and graphs

Ocelote 
Puma
RStudioRStudio is an IDE for R, available at OnDemand web servicesOcelote
RAxMLA program for sequential and parallel Maximum Likelihood based inference of large phylogenetic treesOcelote
Puma
RelionProgram for Maximum A Posteriori refinement in cry-electron microscopyOcelote
RemoraResource Monitoring for Remote ApplicationsOcelote
Puma
RepeatMasker

A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences

Ocelote 
Rings

Rigorous Investigation of Networks Generated using Simulations" is a scientific code developed in Fortran90/MPI to analyze the results of molecular dynamics simulations

Ocelote
RmblastA RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModelerOcelote
Root-CernA modular scientific software frameworkOcelote
Ruby

A dynamic, reflective, object-oriented, general-purpose programming language.

Ocelote 
SalmonA quasi-mapping bioinformatics toolOcelote
Puma
SAMTools

Utilities for manipulating alignments in SAM format

Ocelote 
Puma
SAS

Software suite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.

Ocelote 
Puma
SBTScala build toolOcelote
Puma
ScalaGeneral purpose programming languageOcelote
Puma
SchrodingerLicensed: Molecular modeling and materials science.

Ocelote 

SeqlogoPackage that takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo.Ocelote
ShapeitEstimation of phasing for SNP sequencing dataOcelote
SignalpPackage that 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.Ocelote
Puma
SiloA mesh and field I/O library and scientific databaseOcelote
Puma
SingularitySingularity containers let users run applications in a Linux environment of their choosing.
See tutorial information

ElGato
Ocelote 
Puma**

SlimAn evolutionary simulation software package used for research and teachingOcelote
Puma
SNAPUsed by MakerOcelote 
SOAPdenovo2A novel short-read assembly methodOcelote
SPAdes

St. Petersburg genome assembler, for both standard isolates and single-cell MDA bacteria assemblies

Ocelote 
Puma
Sparsehash

An extremely memory-efficient hash_map implementation

Ocelote 
Puma
SparkFrom Apache.  Open source distributed general-purpose cluster computing framework Ocelote
SpectraC++ library for large scale eigenvalue problemsOcelote
SpeedseqAn open-source genome analysis platform for rapid genome analysis and interpretation Ocelote
SpparksKinetic Monte Carlo simulator from SandiaOcelote
SRAtoolkitEnables reading of sequencing files from the SRA database. From NCBIOcelote
Puma
Stacks

Software pipeline for building loci from short-read sequences

Ocelote
Puma
StarRNA-seq AlignerOcelote 
Puma
StarfusionUses the STAR aligner to identify candidate fusion transcriptsOcelote
TmhmmPackage that predicts transmembrane helices in proteins.Ocelote
Puma
TopHat

Fast splice junction mapper for RNA-Seq reads

Ocelote 
TRF

Telomere Restriction Fragment (TRF) Analysis

Ocelote 
Puma
TrilinosSet of solvers from Sandia National LabsOcelote
Puma
TrimmomaticA flexible trimmer for illumina sequence dataOcelote
Puma
Trinity

Package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data

Ocelote 
Puma
Trinotate

Annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes

Ocelote
UnsupportedAdds user supported software to your module path. On Puma this area is "/contrib"Ocelote
VASP

Atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. Special case: restricted to Engineering and Computer Science

Ocelote 
Puma
VCFtools

Tool providing easily accessible methods for working with complex genetic variation data in the form of VCF files

Ocelote
Velvet

De novo genomic assembler specially designed for short read sequencing technologies

Ocelote
VisitInteractive parallel visualization and graphical analysis tool for viewing scientific dataOcelote
VtuneIntel performance profiler (vtune_amplifier_xe)Ocelote
WGSWhole Genome Shotgun Assembler for the reconstruction of genomic DNA sequence from WGS sequencing dataOcelote
WhamWhole genome Alignment MetricsOcelote
Wien2KSoftware for electronic structure calculations using DFTOcelote
Puma
WRF
WPS 
Weather Research and Forecasting Model.
Special case: available to Hydrology and Atmospheric Sciences
Ocelote
XDMFeXtensible Data Model and FormatOcelote
XzFree general-purpose data compression software with a high compression ratio.Ocelote
Puma**
zlib

A software library used for data compression.

Ocelote
Puma**

** installed on the operating system of each node.  "module load xx" is not necessary.




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