Software
Many computational software packages are installed on our system, and additional packages can be requested by submitting a software request. Note that CCV cannot supply funding for the purchase of commercial software. This is normally attributed as a direct cost of research, and should be purchased with research funding. CCV can help in identifying other potential users of the software to potentially share the cost of purchase and maintenance.
All software listed below can be accessed on CCV systems through the modules environment.
| Name | Version | Module | Description |
| Core Libraries | 5.4 | CoreLib/5.4 | |
| R | 2.11.1 | R/2.11.1 | The R Project for Statistical Computing |
| ABySS | 1.2.5 | abyss/1.2.5 | A De Novo, Parallel, Paired-end Sequence Assembler |
| AFNI | 2008_07_18 | afni/2008_07_18 | Analysis of Functional Neuro Images |
| AFNI | 2010_10_19 | afni/2010_10_19 | Analysis of Functional Neuro Images |
| AFNI | 2011_07_12 | afni/2011_07_12 | Analysis of Functional Neuro Images |
| ARB | 5.2 | arb/5.2 | Sequence Database Handling and Data Analysis |
| ARPACK | 96 | arpack/96 | |
| Aspera Connect | 2.4.5 | aspera/2.4.5 | High Performance Transfer Client |
| ATLAS | 3.9.25 | atlas/3.9.25 | Automatically Tuned Linear Algebra Software |
| AUGUSTUS | 2.5 | augustus/2.5 | Gene Prediction for Eukaryotic Genomic Sequences |
| B2G4PIPE | 2.3.5 | b2g4pipe/2.3.5 | A version for B2G annotation without FrontEnd (GUI) for Pipeline Integration |
| BEAST | 1.6.1 | beast/1.6.1 | Bayesian MCMC Analysis of Molecular Sequences |
| bedtools | 2.12.0 | bedtools/2.12.0 | Flexible suite of utilities for comparing genomic features |
| biomed | 1.0 | biomed/1.0 | some handy customized scripts for bioinformatics |
| BLAST | 2.2.16 | blast/2.2.16 | Basic Local Alignment Search Tool |
| BLAST | 2.2.22 | blast/2.2.22 | Basic Local Alignment Search Tool |
| BLAST | 2.2.24 | blast/2.2.24 | Basic Local Alignment Search Tool |
| BLAST | 2.2.25 | blast/2.2.25 | Basic Local Alignment Search Tool |
| BLAST | 2.2.25-intel | blast/2.2.25-intel | Basic Local Alignment Search Tool |
| Boost | 1.42.0 | boost/1.42.0 | The Boost C++ Libraries |
| Boost | 1.44.0 | boost/1.44.0 | The Boost C++ Libraries |
| Bowtie | 0.12.7 | bowtie/0.12.7 | An Ultrafast Memory-efficient Short Read Aligner |
| Bowtie | 2.2.0beta2 | bowtie/2.2.0beta2 | An Ultrafast Memory-efficient Short Read Aligner |
| bwa | 0.5.9 | bwa/0.5.9 | Burrows-Wheeler Alignment Tool |
| CAP3 | 2007 | cap3/2007 | Sequence Assembly Program |
| CASAVA | 1.7.0 | casava/1.7.0 | Genome Analyzer Software |
| CASAVA | 1.8.0 | casava/1.8.0 | Genome Analyzer Software |
| CatchAll | 3.0 | catchall/3.0 | Analysis of Species Abundance |
| Circos | 0.52-4 | circos/0.52-4 | Circular Genome Data and Annotation Image Generator |
| CitcomS | 3.1.1 | citcoms/3.1.1 | Finite Element Code for Compressible Thermochemical Convection |
| clc-cell | 3.2.2 | clc-cell/3.2.2 | The command-line interface of CLC Assembly Cell |
| 4.6.1 | clc-client/4.6.1 | ||
| Clustal | 2.1 | clustal/2.1 | General Purpose Multiple Sequence Alignment Program for DNA or Proteins |
| CMake | 2.8.2 | cmake/2.8.2 | Cross Platform Make |
| CMake | 2.8.6 | cmake/2.8.6 | Cross Platform Make |
| CNVnator | 0.2.2 | cnvnator/0.2.2 | a tool for CNV discovery and genotyping from depth of read mapping |
| CPLEX | 12.2 | cplex/12.2 | Mathematical Programming Solver |
| CUDA | 3.2.16 | cuda/3.2.16 | GPU Programming Toolkit |
| CUDA | 4.0.17 | cuda/4.0.17 | GPU Programming Toolkit |
| CUDA-BLASTP | 1.0 | cuda-blastp/1.0 | GPU Accelerated BLASTP |
| CUDA-BLASTP | 2.0 | cuda-blastp/2.0 | GPU Accelerated BLASTP |
| CULA | R10 | cula/R10 | GPU-Accelerated Linear Algebra Library |
| tcutadapt | 0.9.4 | cutadapt/0.9.4 | remove adapter sequences from high-throughput sequencing data. |
| deal.II | 7.0.0 | dealii/7.0.0 | Finite Element Differential Equations Analysis Library |
| distmake | 0.5 | distmake/0.5 | Distributed, parallel, GNU make compatible program |
| Emergent | 5.1.0 | emergent/5.1.0 | Neural Network Simulation System |
| Emergent | r4670 | emergent/r4670 | Neural Network Simulation System |
| Emergent | r4752 | emergent/r4752 | Neural Network Simulation System |
| EnSight | 9.2.1c | ensight/9.2.1c | Engineering Visualization Software |
| ERANGE | 3.2.1 | erange/3.2.1 | RNA-seq Analysis |
| ExodusII | 4.96 | exodusii/4.96 | Data Model for Finite Element Analysis |
| Exonerate | 2.2.0 | exonerate/2.2.0 | A Generic Tool for Sequence Alignment |
| fastPHASE | 1.4.0 | fastphase/1.4.0 | Software for Haplotype Reconstruction |
| FastQC | 0.6.1 | fastqc/0.6.1 | Quality Control Application for Sequence Data |
| FastQC | 0.9.2 | fastqc/0.9.2 | Quality Control Application for Sequence Data |
| FFmpeg | 0.6.1 | ffmpeg/0.6.1 | Audio and Video Convertor |
| FFTW | 2.1.5 | fftw/2.1.5 | Fastest Fourier Transform in the West |
| FFTW | 3.2.2 | fftw/3.2.2 | Fastest Fourier Transform in the West |
| FFTW | 3.2.2-intel | fftw/3.2.2-intel | Fastest Fourier Transform in the West |
| FFTW | 3.2.2-pgi | fftw/3.2.2-pgi | Fastest Fourier Transform in the West |
| flex | 2.5.35 | flex/2.5.35 | A Fast Lexical Analyser Generator |
| FreeFem++ | 3.12 | freefem/3.12 | Language for Finite Element Methods |
| FreeSurfer | 4.5.0 | freesurfer/4.5.0 | Automated Tools for MRI Data |
| FreeSurfer | 5.0.0 | freesurfer/5.0.0 | Automated Tools for MRI Data |
| FreeSurfer | 5.1.0 | freesurfer/5.1.0 | Automated Tools for MRI Data |
| FSL | 4.1.4 | fsl/4.1.4 | Analysis Tools for Brain Imaging Data |
| Gaussian09 | g09 | gaussian/g09 | Electronic Structure Modeling |
| Gaussian09 | g09-c01 | gaussian/g09-c01 | Electronic Structure Modeling |
| Gaussian03 | E.01 | gaussian03/E.01 | Electronic Structure Modeling |
| GCC | 4.4.0 | gcc/4.4.0 | GNU Compiler Collection |
| GCC | 4.5.1 | gcc/4.5.1 | GNU Compiler Collection |
| GCC | 4.6.1 | gcc/4.6.1 | GNU Compiler Collection |
| Geant4 | 4.9.4 | geant/4.9.4 | Particle Simulation Toolkit |
| Gecode | 3.7.0 | gecode/3.7.0 | Toolkit for Constraint-Based Systems |
| genenetwork | 0.1 | genenetwork/0.1 | Pipeline for Evolutionary Gene Networks |
| genenetwork | 0.2 | genenetwork/0.2 | Pipeline for Evolutionary Gene Networks |
| Git | 1.7.3.1 | git/1.7.3.1 | Fast Version Control System |
| gmsh | 2.5.0 | gmsh/2.5.0 | 3D Finite Element Mesh Generator |
| gnuplot | 4.4.0 | gnuplot/4.4.0 | Graphing Utility |
| Google Chrome | 12.0.742.124 | google-chrome/12.0.742.124 | Web Browser |
| GotoBLAS2 | 1.13 | gotoblas2/1.13 | Basic Linear Algebra Subroutines |
| GotoBLAS2 | 1.13-pgi | gotoblas2/1.13-pgi | Basic Linear Algebra Subroutines |
| GPU-BLAST | 1.0 | gpu-blast/1.0 | GPU-Accelerated BLASTP |
| GPU-HMMER | 0.92 | gpu-hmmer/0.92 | GPU Accelerated Sequence Homology Search Software |
| graphviz | 2.26.3 | graphviz/2.26.3 | Graph Visualization Software |
| GRIBEX | 370 | gribex/370 | Encoding/Decoding for GRIdded Binary Files |
| HDF5 | 1.8.5 | hdf5/1.8.5 | Hierarchical Data Format 5 (Serial Library) |
| HDF5 | 1.8.7 | hdf5/1.8.7 | Hierarchical Data Format 5 (Serial Library) |
| HDF5 | 1.8.5 | hdf5-par/1.8.5 | Hierarchical Data Format 5 (Parallel Library) |
| HDF5 | 1.8.7 | hdf5-par/1.8.7 | Hierarchical Data Format 5 (Parallel Library) |
| HeliSphere | 1.1 | helisphere/1.1 | Open Source Bioinformatics Software |
| HMMER | 3.0 | hmmer/3.0 | Sequence Homology Search Software |
| Hoard | 3.8 | hoard/3.8 | Memory Allocator Replacement for malloc |
| HPCToolkit | r3338 | hpctoolkit/r3338 | Suite of Performance Tools |
| ImageMagick | 6.6.4 | imagemagick/6.6.4 | Image Manipulation Library |
| intel | 12.0.4 | intel/12.0.4 | Intel Composer XE Compilers and MKL |
| IPM | 2.0.0 | ipm/2.0.0 | Integrated Performance Monitoring |
| IPM | 2.0.0 | ipmio/2.0.0 | Integrated Performance Monitoring (with I/O tracing) |
| ISIS | 3.2.1 | isis/3.2.1 | Planetary Image Processing Software |
| JDK | 6u21 | java/6u21 | Java Developer's Kit (64-bit) |
| Judy | 1.0.5 | judy/1.0.5 | Sparse Dynamic Array Library |
| LAMMPS | 12Sep10 | lammps/12Sep10 | Molecular Dynamics Simulator |
| LAMMPS | 15Dec10 | lammps/15Dec10 | Molecular Dynamics Simulator |
| LAMMPS | 1Jul11-intel | lammps/1Jul11-intel | Molecular Dynamics Simulator |
| libevent | 2.0.13 | libevent/2.0.13 | Event Notification Library |
| likwid | 2.1.3 | likwid/2.1.3 | Lightweight Performance Tools |
| MACS | 1.4.1 | macs/1.4.1 | Model-based Analysis for ChIP-Seq |
| MAGMA | 1.0.0-rc5 | magma/1.0.0-rc5 | Matrix Algebra on GPU and Multicore Architectures |
| MAGMA | 1.0.0-rc5-intel | magma/1.0.0-rc5-intel | Matrix Algebra on GPU and Multicore Architectures |
| MAKER | 2.10 | maker/2.10 | Genome Annotation Pipeline |
| Maple | 15 | maple/15 | Math and Engineering Software |
| maq | 0.7.1 | maq/0.7.1 | Mapping and Assembly with Qualities |
| Mathematica | 7.0.1 | mathematica/7.0.1 | Technical Computing Software |
| Mathematica | 8.0.0 | mathematica/8.0.0 | Technical Computing Software |
| Mathematica | 8.0.1 | mathematica/8.0.1 | Technical Computing Software |
| MATLAB | R2008b | matlab/R2008b | The Language Of Technical Computing |
| MATLAB | R2010b | matlab/R2010b | The Language Of Technical Computing |
| MATLAB | R2011a | matlab/R2011a | The Language Of Technical Computing |
| MCL | 10.201 | mcl/10.201 | a cluster algorithm for graphs |
| MEME | 4.5.0 | meme/4.5.0 | Motif-based Sequence Analysis Tools |
| METIS | 4.0.1 | metis/4.0.1 | Multilevel Partitioning Algorithms |
| MIRA | 3.2.0 | mira/3.2.0 | Whole Genome Shotgun and EST Sequence Assembler |
| MIRA | 3.2.1 | mira/3.2.1 | Whole Genome Shotgun and EST Sequence Assembler |
| mirexpress | 2.1.3 | mirexpress/2.1.3 | Analyzing high-throughput sequencing data for profiling microRNA expression |
| MNE | 2.7.2 | mne/2.7.2 | MEG and EEG Preprocessing Tools |
| mpiBLAST | 1.6.0 | mpiblast/1.6.0 | Open-Source Parallel BLAST |
| MPICH2 | 1.3.2p1 | mpich2/1.3.2p1 | Message Passing Library |
| MPlayer | r32713 | mplayer/r32713 | Movie Player |
| MrBayes | 3.1.2 | mrbayes/3.1.2 | Bayesian Inference of Phylogeny |
| MrBayes | 3.1.2h | mrbayes/3.1.2h | Bayesian Inference of Phylogeny |
| MRIcron | 2011_04_01 | mricron/2011_04_01 | Analysis Tool for Brain Imaging Data |
| Multidistribute | 09.25.03 | multidistribute/09.25.03 | Rates of Molecular Evolution |
| MUMPS | 4.9.2 | mumps/4.9.2 | Multifrontal Massively Parallel Sparse Direct Solver |
| MUSCLE | 3.8.31 | muscle/3.8.31 | Multiple Sequence Alignment |
| MySQL | 5.5.9 | mysql/5.5.9 | Open Source Database |
| NAG | 5.2 | nagfor/5.2 | Numerical Algorithm Group Fortran Compiler |
| NAG | 2011 | naglib/2011 | Numerical Algorithm Group Libraries |
| NASA Ames Stereo Pipeline | 1.0.4 | nasa-asp/1.0.4 | Automated Geodesy & Stereogrammetry Tools |
| NCL | 6.0.0 | ncl/6.0.0 | NCAR Command Language |
| netCDF | 3.6.3 | netcdf/3.6.3 | Network Common Data Format |
| netCDF | 4.1.1 | netcdf/4.1.1 | Network Common Data Format |
| NWChem | 6.0 | nwchem/6.0 | High-Performance Computational Chemistry Tool |
| NWChem | 6.0-p | nwchem/6.0-p | High-Performance Computational Chemistry Tool |
| OLB | 1.8.0 | olb/1.8.0 | Off-line Base Caller |
| OLB | 1.9.0 | olb/1.9.0 | Off-line Base Caller |
| OLB | 1.9.3 | olb/1.9.3 | Off-line Base Caller |
| OpenBUGS | 3.1.2 | openbugs/3.1.2 | Bayesian Inference Using Gibbs Sampling |
| OpenCV | 2.1.0 | opencv/2.1.0 | Open Source Computer Vision Library |
| OpenCV | 2.2.0 | opencv/2.2.0 | Open Source Computer Vision Library |
| OpenFOAM | 2.0.1 | openfoam/2.0.1 | Open source CFD toolbox |
| OpenMPI | 1.2.8 | openmpi/1.2.8 | Message Passing Library |
| OpenMPI | 1.2.8-pgi | openmpi/1.2.8-pgi | Message Passing Library |
| OpenMPI | 1.4.3 | openmpi/1.4.3 | Message Passing Library |
| OpenMPI | 1.4.3-intel | openmpi/1.4.3-intel | Message Passing Library |
| OpenMPI | 1.4.3-pgi | openmpi/1.4.3-pgi | Message Passing Library |
| OrthoMCL | 2.0.2 | orthomcl/2.0.2 | Genome-scale Algorithm for Grouping Orthologous Protein Sequences |
| PAML | 4.4c | paml/4.4c | Phylogenetic Analysis by Maximum Likelihood |
| ParaView | 3.8.1 | paraview/3.8.1 | Data Analysis and Visualization |
| ParMETIS | 3.1.1 | parmetis/3.1.1 | Parallel Graph Partitioning |
| PeakSplitter | 1.0 | peaksplitter/1.0 | Subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks |
| PeakSplitter | 1.0 | peaksplitter_java/1.0 | Subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks |
| Perl | 5.12.2 | perl/5.12.2 | The Perl Programming Language |
| Perl | 5.8.8 | perl/5.8.8 | The Perl Programming Language |
| PETSc | 3.0.0-p12 | petsc/3.0.0-p12 | Portable, Extensible Toolkit for Scientific Computation |
| PGI | 11.4 | pgi/11.4 | Portland Group Compiler Suite |
| PGI | 8.0-6 | pgi/8.0-6 | Portland Group Compiler Suite |
| PHASE | 2.1.1 | phase/2.1.1 | Software for Haplotype Reconstruction |
| phrap | 0.990329 | phrap/0.990329 | Assembler for Shotgun DNA Sequence Data |
| phrap | 1.090518 | phrap/1.090518 | Assembler for Shotgun DNA Sequence Data |
| PLINK | 1.07 | plink/1.07 | Whole Genome Association Analysis Toolset |
| PyPy | 1.6 | pypy/1.6 | Fast, Alternative Implementation of Python |
| Python | 2.6.6 | python/2.6.6 | The Python Programming Language |
| Python | 2.7.2 | python/2.7.2 | The Python Programming Language |
| Python | 3.2.2 | python/3.2.2 | The Python Programming Language |
| QIIME | 1.3.0 | qiime/1.3.0 | Quantitative Insights Into Microbial Ecology |
| Qt | 4.7.1 | qt/4.7.1 | Cross-Platform Application and UI Framework |
| RAxML | 7.0.4 | raxml/7.0.4 | Randomized Accelerated Maximum Likelihood |
| RAxML | 7.2.6 | raxml/7.2.6 | Randomized Accelerated Maximum Likelihood |
| Ray | 1.2.0 | ray/1.2.0 | De Novo Assembler Using MPI |
| RepeatMasker | 3.2.9 | repeatmasker/3.2.9 | Screens DNA Sequences for Interspersed Repeats |
| Root | 5.28 | root/5.28 | A Data Analysis Framework |
| RStudio | 0.94.105 | rstudio/0.94.105 | Integrated Development Environment (IDE) for R |
| SAMtools | 0.1.12a | samtools/0.1.12a | Sequence Alignment/Map Format |
| SAMtools | 0.1.16 | samtools/0.1.16 | Sequence Alignment/Map Format |
| SAMtools | 0.1.8 | samtools/0.1.8 | Sequence Alignment/Map Format |
| 1.8.0 | scalapack/1.8.0 | ||
| SeqAn | 1.3 | seqan/1.3 | C++ Library for the Analysis of Sequences |
| Shogun | 0.10.0 | shogun/0.10.0 | A Large Scale Machine Learning Toolbox |
| Shogun | 0.9.3 | shogun/0.9.3 | A Large Scale Machine Learning Toolbox |
| Siesta | 2.0.2 | siesta/2.0.2 | A Linear-Scaling Density-Functional Method |
| Silo | 4.8 | silo/4.8 | Mesh and Field I/O Library |
| simNGS | 1.5.1 | simngs/1.5.1 | Software for Simulating Next-Gen Sequencing Data |
| SNPHAP | 1.3.1 | snphap/1.3.1 | Estimating Frequencies of Haplotypes |
| SOAPdenovo | 1.04 | soapdenovo/1.04 | De Novo Draft Assembly for Human-Sized Genomes |
| SOAPdenovo | 1.05 | soapdenovo/1.05 | De Novo Draft Assembly for Human-Sized Genomes |
| Splus | 8.0.4 | splus/8.0.4 | Statistical Analysis Software |
| SPRNG | 4.0 | sprng/4.0 | Scalable Parallel Pseudo Random Number Generators Library |
| SQLite | 3.7.7.1 | sqlite/3.7.7.1 | Self-contained SQL Database Engine |
| SRA | 2.1.4 | sra/2.1.4 | Toolkit for Sequence Data |
| STATA | 12 | stata/12 | Data Analysis and Statistical Software |
| SuiteSparse | 3.4.0 | suitesparse/3.4.0 | Sparse Matrix Packages |
| syzygy | 1.1.0 | syzygy/1.1.0 | Framework for Identification/Characterization of Genetic Variants |
| TAU | 2.20.2 | tau/2.20.2 | Tuning and Analysis Utilities |
| TBB | 3.0 | tbb/3.0 | Intel Thread Building Blocks |
| Tecplot 360/Focus | 2008 | tecplot/2008 | Visualization and Plot Software |
| Globus | 5.0.3 | teragrid/5.0.3 | TeraGrid Client |
| TeX Live | 2010 | texlive/2010 | Comprehensive TeX Distribution |
| TotalView | 8.9.0-2 | totalview/8.9.0-2 | Parallel Debugger |
| Trilinos | 10.2.2 | trilinos/10.2.2 | Algorithms for Engineering and Scientific Problems |
| Trinity | 20110519 | trinity/20110519 | RNA-Seq De Novo Assembly |
| Trinity | 20110713 | trinity/20110713 | RNA-Seq De Novo Assembly |
| TurboVNC | 1.0.1 | turbovnc/1.0.1 | High Performance Virtual Network Computing |
| TurboVNC | 1.0.2 | turbovnc/1.0.2 | High Performance Virtual Network Computing |
| Valgrind | 3.6.0 | valgrind/3.6.0 | Debugging and Profiling System |
| VASP | 4.6.36 | vasp/4.6.36 | Vienna Ab-initio Simulation Package |
| VASP | 4.6.36-atlas | vasp/4.6.36-atlas | Vienna Ab-initio Simulation Package |
| VASP | 4.6.36-pgi | vasp/4.6.36-pgi | Vienna Ab-initio Simulation Package |
| VASP | 5.2.2 | vasp/5.2.2 | Vienna Ab-initio Simulation Package |
| VASP | 5.2.2-pgi | vasp/5.2.2-pgi | Vienna Ab-initio Simulation Package |
| vcftools | 0.1.5 | vcftools/0.1.5 | a program package designed for working with VCF files |
| Velvet | 1.1.04 | velvet/1.1.04 | Sequence Assembler for Very Short Reads |
| Velvet | 1.1.04-intel | velvet/1.1.04-intel | Sequence Assembler for Very Short Reads |
| VirtualGL | 2.2.90 | virtualgl/2.2.90 | Remote display software with OpenGL hardware acceleration |
| VisIt | 2.2.0 | visit/2.2.0 | Parallel Visualization and Analysis Package |
| VisIt | 2.3.1 | visit/2.3.1 | Parallel Visualization and Analysis Package |
| ScaleMP | beta-.99 | vsmp/beta-.99 | commercial virtual SMP package |
| VTK | 5.6.0 | vtk/5.6.0 | The Visualization Toolkit |
| YASRA | 2010.02.27 | yasra/2010.02.27 | Comparative Genome Assembler |