Software Applications
Modules
Modules allow you to set up your current environment to suit whatever application or library you wish to use. It is also a convenient way to determine what applications and versions of those applications are available. Here is a brief list of the module commands -
- module avail - to list all the applications (and similar) that modules can help you with.
- module load blas - to set up your environment to use the default blas libraries (use any of the terms discovered with the above command). This will remain in effect until you logoff (or unload).
How To Apply Restricted Software
To applying restricted software, please link the following page:
https://help.vlsci.unimelb.edu.au/user/
Then: Restricted Software > Add software > Find the software you need > Read and accept the license.
Software Applications
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ABySS VERSION(s): 1.1.2, 1.2.7 DESCRIPTION: De novo, parallel, paired-end sequence assembler. |
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ALLPATHS-LG VERSION(s): 39433, 40324 DESCRIPTION: The ALLPATHS-LG assembly of Ground Squirrel (thirteen-lined) (Spermophilus tridecemlineatus) |
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Amber VERSION(s): 11 DESCRIPTION: Molecular simulation and force fields. |
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Amber VERSION(s): 11 DESCRIPTION: Molecular simulation and force fields. |
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AmberTools VERSION(s): 1.3 1.4 1.5 DESCRIPTION: Molecular simulation and force fields. |
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AmberTools VERSION(s): 1.4 DESCRIPTION: Molecular simulation and force fields. |
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Ant VERSION(s): 1.8.1 DESCRIPTION: Java software build tool. |
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ANTLR VERSION(s): 3.1.3 DESCRIPTION: Parser generator. |
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ANTS VERSION(s): 1.9.1 DESCRIPTION: Brain and image mapping. |
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AnyExpress VERSION(s): 1.0 DESCRIPTION: An integrated toolkit for cross-platform gene expression data |
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armadillo VERSION(s): 2.2.4 DESCRIPTION: Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK, or one of its high performance drop-in replacements (such as MKL or ACML). |
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ATK VERSION(s): 1.32.0 DESCRIPTION: Gnome accessibility toolkit. |
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ATLAS VERSION(s): 3.8.3, 3.9.32 DESCRIPTION: Automatically tuned linear algebra software. |
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autoconf VERSION(s): 2.65 2.68 DESCRIPTION: Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. |
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AutoDock VERSION(s): 4.2.3 DESCRIPTION: Prediction of how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. |
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AutoDock VERSION(s): 4.2 DESCRIPTION: Prediction of how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. |
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automake VERSION(s): 1.11 1.11.1 DESCRIPTION: Automake is a tool for automatically generating `Makefile.in' files compliant with the GNU Coding Standards. |
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BAMBUS VERSION(s): 2.33 DESCRIPTION: Bambus is the first general purpose scaffolder that is publicly available as an open source package. |
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BamTools VERSION(s): 2.0.5; 2.1.1 DESCRIPTION: BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files. |
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BAPS VERSION(s): 5.3 DESCRIPTION: Bayesian Analysis of Population Structure |
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BaTS VERSION(s): 1.0 DESCRIPTION: Bayesian Tip-Significance testing. |
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Beagle VERSION(s): 20120221 DESCRIPTION: BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics package. |
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BEAST VERSION(s): 1.5.4, 1.6.1, 1.7.1 DESCRIPTION: Bayesian MCMC analysis of molecular sequences. |
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BedTools VERSION(s): 2.9.0 2.12.0 DESCRIPTION: Processing BED, GFF/GTF, VCF, and SAM/BAM files for common genomics tasks such as finding feature overlaps and computing coverage. |
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BFAST VERSION(s): 0.6.4c, 0.6.4e, 0.6.5a, 0.7.0a DESCRIPTION: Mapping NGS short reads to a reference genome. |
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binutils VERSION(s): 2.19.92 2.20.1 DESCRIPTION: The GNU Binutils are a collection of binary tools. |
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Bio-SamTools VERSION(s): 1.29 DESCRIPTION: This is a Perl interface to the SAMtools sequence alignment interface |
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Bio::Perl VERSION(s): 1.6.1 DESCRIPTION: Perl modules targetting life sciences applications. |
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Bioscope VERSION(s): 1.2, 1.3.1 DESCRIPTION: Pipeline for processing SOLiD NGS sequence data. |
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BJam VERSION(s): 3.1.18 DESCRIPTION: Boost provides free portable peer-reviewed C++ libraries. The emphasis is on portable libraries which work well with the C++ Standard Library. |
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BLAS VERSION(s): 20110419 DESCRIPTION: Linear algebra library. |
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BLAST VERSION(s): 2.2.23, 2.2.24 DESCRIPTION: Find regions of similarity between biological sequences. |
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BLAST+ VERSION(s): 2.2.22, 2.2.23, 2.2.24, 2.2.25 DESCRIPTION: Protein database sequence search. |
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blat VERSION(s): 34 DESCRIPTION: UCSC Genome Bioinformatics Group's suite of biological analysis and web display programs. |
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Boost VERSION(s): 1.47.0, 1.49.0 DESCRIPTION: C++ libraries. |
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Boost VERSION(s): 1.34.1, 1.34.1.32, 1.42.0, 1.45.0 DESCRIPTION: C++ libraries. |
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Bowtie VERSION(s): 0.12.3, 0.12.5, 0.12.7 DESCRIPTION: Mapping NGS short reads to a reference genome. |
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bpipe VERSION(s): 0.9.5.3 DESCRIPTION: A tool for running and managing bioinformatics pipelines. |
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breakdancer VERSION(s): 1.1_2011_02_21 DESCRIPTION: Provides genome-wide detection of structural variants from next generation paired-end sequencing reads |
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Bucky VERSION(s): 1.4.0 DESCRIPTION: BUCKy is a free program to combine molecular data from multiple loci |
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BWA VERSION(s): 0.5.7; 0.5.9; 0.6.1; 0.6.2 DESCRIPTION: Mapping NGS short reads to a reference genome. |
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Cairo VERSION(s): 1.10.2, 1.6.4 DESCRIPTION: 2D graphics library. |
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CAP3 VERSION(s): 10.15.07 DESCRIPTION: DNA sequence assembly. |
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Charm++ VERSION(s): 6.4 DESCRIPTION: An object-orientated portable parallel language built on top of C++. |
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Charm++ VERSION(s): 6.1.3, 6.2.1 DESCRIPTION: An object-orientated portable parallel language built on top of C++. |
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chaste VERSION(s): 2.3 DESCRIPTION: Chaste (Cancer, Heart and Soft Tissue Environment) is a general purpose simulation package aimed at multi-scale, computationally demanding problems arising in biology and physiology. |
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Chimera VERSION(s): 1.4 DESCRIPTION: Interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories and conformational ensembles. |
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ClustalW VERSION(s): 2.1 DESCRIPTION: Multiple alignment of nucleic acid and protein sequences |
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CMake VERSION(s): 2.8.0 DESCRIPTION: Software build system. |
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CMake VERSION(s): 2.8.3 DESCRIPTION: Software build system. |
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COMSOL Multiphysics VERSION(s): 4.1 DESCRIPTION: Multiphysics package. |
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CONTRA VERSION(s): 2.0.2 DESCRIPTION: CONTRA is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data. |
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Cortex VERSION(s): 0.04c, 1.0.5.3; DESCRIPTION: Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. There are two main executables, being developed in parallel streams: cortex_con (primary contact Mario Caccamo) is for consensus genome assembly, and cortex_var (primary contact Zamin Iqbal) is for variation and population assembly. |
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Cppcheck VERSION(s): 1.47 DESCRIPTION: Static analysis tool for C/C++ source code. |
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crest VERSION(s): 20110810 DESCRIPTION: CREST is a new algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data. |
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Cufflinks VERSION(s): 1.0.3 DESCRIPTION: Transcript assembly and mapping using Bowtie |
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Dalton VERSION(s): 2011 DESCRIPTION: The DALTON code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDALTON is a linear-scaling HF and DFT code suitable for large molecular systems. |
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DDD VERSION(s): 3.3.12 DESCRIPTION: Program debugger with graphics interface. |
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Desmond VERSION(s): 2.4.2.1 DESCRIPTION: Molecular dynamics |
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Dindel VERSION(s): 1.01 DESCRIPTION: A program for calling small indels from short-read sequence data ('next generation sequence data'). It is currently designed to handle only Illumina data. |
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Dock VERSION(s): 6.3 DESCRIPTION: Molecular docking tool |
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DTK VERSION(s): 0.6 DESCRIPTION: Data reconstruction and fiber tracking on diffusion MR images |
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EMAN VERSION(s): 2rc3 DESCRIPTION: Scientific image processing tool aimed primarily at the transmission electron microscopy community |
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Emboss VERSION(s): 6.3.1 DESCRIPTION: European molecular biology open software suite |
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Ensembl VERSION(s): 20100514; 64; 67 DESCRIPTION: Genome databases for vertebrates and other eukaryotic species |
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epm VERSION(s): 4.1 DESCRIPTION: EPM is the software packaging tool that we now use at Easy Software Products. |
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ESPResSo VERSION(s): 3.1.0 DESCRIPTION: is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, ferrofluids and biological systems, for example DNA and lipid membranes. |
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est2assembly VERSION(s): 1.05 DESCRIPTION: Assembly and annotation of transcriptomes for any species |
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ESTScan VERSION(s): 3.0.3 DESCRIPTION: Detection of coding regions in DNA sequences, even if they are of low quality. |
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Exonerate VERSION(s): 2.2.0 DESCRIPTION: Generic tool for pairwise sequence comparison (sequence alignment) |
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Expat VERSION(s): 2.0.1 DESCRIPTION: A library for parsing XML |
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FastEpistasis VERSION(s): 1.07 DESCRIPTION: FastEpistasis , a software tool capable of computing tests of epistasis for a large number of SNP pairs, is an efficient parallel extension to the PLINK epistasis module. |
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FastQC VERSION(s): 0.9.1 0.10.1 DESCRIPTION: FastQC is a quality control application for high throughput sequence data. |
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FASTX-Toolkit VERSION(s): 0.0.13 DESCRIPTION: The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. |
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FFmpeg VERSION(s): 0.7 DESCRIPTION: FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. It includes libavcodec - the leading audio/video codec library. |
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FFTW VERSION(s): 2.1.5, 3.2.1 DESCRIPTION: A fast, free C FFT library; includes real-complex, multidimensional and parallel transforms |
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FFTW VERSION(s): 2.1.5, 3.2.2 DESCRIPTION: A fast, free C FFT library; includes real-complex, multidimensional and parallel transforms. |
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fio VERSION(s): 1.41 DESCRIPTION: Fio is a tool that will spawn a number of threads or processes doing a particular type of io action as specified by the user. |
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Flex VERSION(s): 2.5.35 DESCRIPTION: A tool for generating lexical scanners. |
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Fontconfig VERSION(s): 2.5.91 DESCRIPTION: Fontconfig is a library for configuring and customizing font access. |
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FrameDP VERSION(s): 1.0.3 DESCRIPTION: Sensitive peptide detection on noisy matured sequences. |
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FreeBayes VERSION(s): 20120808 DESCRIPTION: FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. |
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FreeSurfer VERSION(s): 4.5.0, 5.0.0, 5.1.0 DESCRIPTION: Tools for reconstruction of the brain's cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface. |
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FSL VERSION(s): 4.1.5 DESCRIPTION: Library of analysis tools for FMRI, MRI and DTI brain imaging data. |
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FusionSeq VERSION(s): 0.6.1 DESCRIPTION: A modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data |
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GAMESS VERSION(s): 25 MAR 2010 (R2), 12 JAN 2009 (R3) DESCRIPTION: Ab initio quantum chemistry package |
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GAMESS VERSION(s): 25 Mar 2010 (R2) DESCRIPTION: Ab initio quantum chemistry package |
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GATK VERSION(s): 1.0.4013 1.0.4418 1.0.5336 1.0.5777 1.1-30 1.2-2 1.5-9 1.5-25 1.6-7 DESCRIPTION: The Genome Analysis Toolkit |
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GCC VERSION(s): 4.4.3, 4.4.4, 4.6.0 DESCRIPTION: Compilers for C, Fortran and C++ |
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GCC-fe VERSION(s): 4.3.2 DESCRIPTION: Compilers for C, Fortran and C++ |
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GDAL VERSION(s): 1.9.0 DESCRIPTION: Geospatial Data Abstraction Library |
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GDK-PixBuf VERSION(s): 2.22.0 DESCRIPTION: GdkPixbuf is a library for image loading and manipulation. |
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gettext VERSION(s): 0.18.1.1 DESCRIPTION: This package offers to programmers, translators, and even users, a well integrated set of tools and documentation. Specifically, the GNU `gettext' utilities are a set of tools that provides a framework to help other GNU packages produce multi-lingual messages. |
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GHC VERSION(s): 6.12.3 DESCRIPTION: Haskell compiler and interpreter |
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Git VERSION(s): 1.7.0.2 DESCRIPTION: Software revision control |
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Git VERSION(s): 1.7.2.1 DESCRIPTION: Software revision control |
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Glib2 VERSION(s): 2.22.0 2.27.0 DESCRIPTION: GLib is the low-level core library that forms the basis for projects such as GTK+ and GNOME. |
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GMP VERSION(s): 5.0.1 DESCRIPTION: Multiple precision arithmetic library. |
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GMP VERSION(s): 4.2.4 DESCRIPTION: Multiple precision arithmetic library. |
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Gnuplot VERSION(s): 4.4.0 DESCRIPTION: Graph drawing. |
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gossamer VERSION(s): 1.2.1-r; 1.2.2-r DESCRIPTION: Gossamer is an application for the de novo assembly of genomes from fragments of DNA that specifically attacks the question of scalability. |
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Graphviz VERSION(s): 2.26.3 DESCRIPTION: Graph drawing. |
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Gromacs VERSION(s): 3.3.3, 4.0.7, 4.5.1, 4.5.3, 4.5.4 4.5.5 4.6.1 DESCRIPTION: Parallel molecular dynamics software |
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Gromacs VERSION(s): 4.0.7, 4.5.1 4.5.3 4.5.4 4.5.5 DESCRIPTION: Parallel molecular dynamics software. |
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Gromacs VERSION(s): 4.0.7; 4.5.4; 4.5.5 DESCRIPTION: Parallel molecular dynamics software |
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gsl VERSION(s): 1.14 DESCRIPTION: GSL, the GNU Scientific Library, a collection of numerical routines for scientific computing. |
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gtk VERSION(s): 2.22.0 DESCRIPTION: GTK+ is a multi-platform toolkit for creating graphical user interfaces. |
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Hadoop VERSION(s): 0.20.1 0.20.203.0 DESCRIPTION: A framework that allows for the distributed processing of large data sets across clusters of computers using a simple programming model. |
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Haploview VERSION(s): 4.1 DESCRIPTION: Haplotype analysis package |
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Haskell platform VERSION(s): 2010.2.0.0 DESCRIPTION: Standard software libraries for Haskell. |
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HDF5 VERSION(s): 1.8.4-patch1 DESCRIPTION: Data model, library, and file format for storing and managing data |
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HDF5 VERSION(s): 1.8.7 DESCRIPTION: Data model, library, and file format for storing and managing data |
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HMMER VERSION(s): 3.0 DESCRIPTION: Biosequence analysis using profile hidden Markov models. |
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HPL VERSION(s): 2.0 DESCRIPTION: High performance computing linpack benchmark |
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hwloc VERSION(s): 0.9.3, 1.0rc1, 1.1.1 DESCRIPTION: Portable hardware locality. Tool for gathering information about modern computing hardware so as to exploit it accordingly and efficiently. |
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HyPhy VERSION(s): 2011.05.30 DESCRIPTION: Molecular evolution and statistical sequence analysis |
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iAssembler VERSION(s): 1.3 DESCRIPTION: iAssembler is a standalone package to assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs. |
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IGV VERSION(s): 1.5.52 2.0.5 DESCRIPTION: Interactive genomics viewer |
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IGVtools VERSION(s): 1.5.15 DESCRIPTION: Utilities for preprocessing data files for IGV |
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IMA2 VERSION(s): 8.27.12 DESCRIPTION: IMa2 is a progam ( writen with Sang Chul Choi and Rasmus Nielsen) that extends the method of Hey and Nielsen (2007) to two or more populations. |
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ImageMagick VERSION(s): 6.6.5-10 DESCRIPTION: Create, edit, compose, or convert bitmap images. |
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Intel compilers VERSION(s): 11.1, 12.0, 12.1, 12.1.2, 12.1.3, 12.1.5 DESCRIPTION: Compilers for C, C++ and Fortran. |
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InterProScan VERSION(s): 4.6 DESCRIPTION: A tool that combines different protein signature recognition methods native to the InterPro member databases into one resource with look up of corresponding InterPro and GO annotation |
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ITAC VERSION(s): 8.0.0.011 DESCRIPTION: Intel trace analyzer and collector. |
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ITK VERSION(s): 3.16.0, 3.20.0 DESCRIPTION: Software tools for image analysis |
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Java VERSION(s): 1.6.0_20, 1.6.0_25 DESCRIPTION: Compiler and runtime environment for Java. |
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Jweb VERSION(s): 19.00 DESCRIPTION: JWeb is a point-and-click interface for display and interaction with SPIDER images and data. |
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kobas VERSION(s): 1.2.0 DESCRIPTION: KEGG Orthology Based Annotation System (KOBAS) is a standalone Python application in Bioinformatics. |
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KyotoCabinet VERSION(s): 1.2.70 DESCRIPTION: Kyoto Cabinet is a library of routines for managing a database. |
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LAMMPS VERSION(s): 15 Jan 2011 DESCRIPTION: Molecular dynamics code, an anacronym for Large-scale Atomic/Molecular Massively Parallel simulator |
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LAMMPS VERSION(s): 15Jan11 DESCRIPTION: Classical molecular dynamics simulation. LAMMPS, is an anacronym for Large-scale Atomic/Molecular Massivley Parallel Simulator. |
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lapack VERSION(s): 3.2.1 DESCRIPTION: LAPACK is a library of Fortran 90 with subroutines for solving the most commonly occurring problems in numerical linear algebra. It is freely-available software, and is copyrighted. |
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lapack VERSION(s): 3.2.2 DESCRIPTION: LAPACK is a library of Fortran 90 with subroutines for solving the most commonly occurring problems in numerical linear algebra. It is freely-available software, and is copyrighted. |
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Libtool VERSION(s): 2.4 DESCRIPTION: This is GNU Libtool, a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. |
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liftover VERSION(s): 20110517 DESCRIPTION: This tool converts genome coordinates and genome annotation files between assemblies. |
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LLVM VERSION(s): 2.9 DESCRIPTION: The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. |
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M4 VERSION(s): 1.4.16 DESCRIPTION: m4 is an implementation of the traditional Unix macro processor. |
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MACS VERSION(s): 1.3.7.1 DESCRIPTION: Model-based Analysis for Ch IP-Seq |
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MAFFT VERSION(s): 6.951 DESCRIPTION: Multiple alignment program for amino acid or nucleotide sequences |
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Make VERSION(s): 3.82 DESCRIPTION: Source build tool for front-end node. Updated from default system version |
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MAQ VERSION(s): 0.6.6, 0.7.1 DESCRIPTION: Software for mapping assemblies from short reads generated by the next generation sequencing machines |
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MATLAB VERSION(s): R2010a R2011a DESCRIPTION: MATLAB is a general purpose analysis and graphics package with lots of toolboxes. |
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maven VERSION(s): 3.0 DESCRIPTION: Maven is a software project management and comprehension tool. |
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Medinria VERSION(s): 1.9.0 DESCRIPTION: Medical image processing and visualisation |
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MEME VERSION(s): 4.6.1 DESCRIPTION: A software package to discover motifs (highly conserved regions) in groups of related DNA or protein sequences and, search sequence databases using motifs. |
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Mercurial VERSION(s): 1.8.2 DESCRIPTION: Free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. |
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Mesa VERSION(s): 7.7.1 DESCRIPTION: 3-D graphics library |
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MGLtools VERSION(s): 1.5.4 DESCRIPTION: MGLTools is a software developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures. |
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Migrate-n VERSION(s): 3.2.16 DESCRIPTION: Estimation of population sizes and gene flow using the coalescent |
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Mira VERSION(s): 3.0.3, 3.2.1 3.2.1.18 3.4.0 DESCRIPTION: A whole genome shotgun and EST sequence assembler for Sanger, 454 and Solexa/ Illumina data |
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Mosaik VERSION(s): 1.0.1388 DESCRIPTION: A reference guided sequence assembler |
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Mothur VERSION(s): 1.8 DESCRIPTION: Software for describing and comparing microbial communities |
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mothur VERSION(s): 1.8, 1.30.2 DESCRIPTION: This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. |
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mpc VERSION(s): 0.9 DESCRIPTION: Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result |
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mpc VERSION(s): 0.8.2 DESCRIPTION: Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result |
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mpfr VERSION(s): 2.4.2 DESCRIPTION: The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. |
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mpfr VERSION(s): 2.4.2, 3.1.0 DESCRIPTION: The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. |
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mpiBLAST VERSION(s): 1.6.0 DESCRIPTION: Sequencing: parallel implementation of NCBI BLAST |
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mpiBLAST VERSION(s): 1.6.0 DESCRIPTION: Sequencing: parallel implementation of NCBI BLAST |
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MPIBZIP2 VERSION(s): 0.6 DESCRIPTION: MPIBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses MPI and achieves significant speedup on cluster machines |
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MrBayes VERSION(s): 3.1.2 DESCRIPTION: A program for the Bayesian estimation of phylogeny |
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MUMmer VERSION(s): 3.22 DESCRIPTION: MUMmer is a system for rapidly aligning entire genomes. |
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MUSCLE VERSION(s): 3.80.22 DESCRIPTION: Multiple sequence alignment |
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NAMD VERSION(s): 2.6; 2.7; 2.7b1; 2.7b2; 2.7b3; 2.8; 2.8b1; 2.9 DESCRIPTION: Parallel molecular dynamics software. |
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NAMD VERSION(s): 2.9 DESCRIPTION: Parallel molecular dynamics software |
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NAMD VERSION(s): 2.9b3 DESCRIPTION: Parallel molecular dynamics software |
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NetCDF VERSION(s): 4.0.1 DESCRIPTION: The Unidata network Common Data Form (netCDF) is an interface for scientific data access and a freely-distributed software library that provides an implementation of the interface. |
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Neuron VERSION(s): 7.1 DESCRIPTION: Empirically-based simulations of neurons and networks of neurons |
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Neuron VERSION(s): 7.1 DESCRIPTION: Empirically-based simulations of neurons and networks of neurons. |
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Novoalign VERSION(s): 2.05.32; 2.08.01 DESCRIPTION: Aligner for single and paired end short reads |
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Octave VERSION(s): 3.2.4 DESCRIPTION: A high-level language, primarily intended for numerical calculations |
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OpenFOAM VERSION(s): 1.6 1.7 2.0.x-gcc 2.0.1-gcc DESCRIPTION: Computational fluid dynamics tool box |
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OpenFOAM VERSION(s): 2.0.1 DESCRIPTION: Computational fluid dynamics tool box. |
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openmpi VERSION(s): 1.4.1 1.4.2 DESCRIPTION: The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners. |
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OpenSim VERSION(s): 2.2.1 DESCRIPTION: OpenSim is a freely available, user extensible software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement. |
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PAML VERSION(s): 4.4 DESCRIPTION: PAML (for Phylogentic Analysis by Maximum Likelihood) contains a few programs for model fitting and phylogenetic tree reconstruction using nucleotide or amino-acid sequence data |
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Pango VERSION(s): 1.21.0 1.28.0 DESCRIPTION: Pango is a library for layout and rendering of text, with an emphasis on internationalization. |
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paraview VERSION(s): 3.6.1, 3.14 DESCRIPTION: ParaView is an open-source, multi-platform data analysis and visualization application. Part of Openfoam |
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paraview VERSION(s): 3.8.1 DESCRIPTION: ParaView is an open-source, multi-platform data analysis and visualization application. Part of Openfoam |
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pBWA VERSION(s): 0.5.9-r30 DESCRIPTION: Parallel implementation of BWA (http://bio-bwa.sourceforge.net/) using the OpenMPI library |
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PBZIP2 VERSION(s): 1.1.4 DESCRIPTION: A parallel implementation of the bzip2 block-sorting file compressor. |
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Perl VERSION(s): 5.10.1 DESCRIPTION: General purpose powerful scripting language with lots of modules available |
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Perl VERSION(s): 5.8.9, 5.10.1 DESCRIPTION: general purpose powerful scripting language with lots of modules available. |
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PETSc VERSION(s): 3.1-p3, 3.1-p8 DESCRIPTION: A suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. |
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phrap VERSION(s): 0.990329 DESCRIPTION: phrap is a program for assembling shotgun DNA sequence data. |
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phred VERSION(s): 020425 DESCRIPTION: The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base. |
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PHYLIP VERSION(s): 3.69 DESCRIPTION: PHYLIP is a free package of programs for inferring phylogenies. |
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Picard VERSION(s): 1.17 1.29 1.53 DESCRIPTION: Picard comprises 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 |
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pigz VERSION(s): 2.1.6 DESCRIPTION: A parallel implementation of gzip for modern multi-processor, multi-core machines |
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pindel VERSION(s): 20110309 DESCRIPTION: Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. |
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pixman VERSION(s): 0.21.4 DESCRIPTION: pixman is a library that provides low-level pixel manipulation features such as image compositing and trapezoid rasterization. |
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PLINK VERSION(s): 1.07 DESCRIPTION: Whole genome association analysis toolset |
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POVRay VERSION(s): 3.6.1 DESCRIPTION: The Persistence of Vision Raytracer is a high-quality, totally free tool for creating stunning three-dimensional graphics. |
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price VERSION(s): 0.0 0.10 0.4 0.5 0.9 0.12 DESCRIPTION: PRICE uses paired-read information to iteratively increase the size of existing contigs. |
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PROJ.4 VERSION(s): 4.8.0 DESCRIPTION: Cartographic Projections Library |
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PROTTEST VERSION(s): 2.4 DESCRIPTION: PROTTEST (ModelTest's relative) is a program for selecting the model of protein evolution that best fits a given set of sequences (alignment). |
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Prunier VERSION(s): 2.1 DESCRIPTION: Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests |
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PYPY VERSION(s): 1.9.0 DESCRIPTION: PyPy is a fast, compliant alternative implementation of the Python language (2.7.2). |
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PyTables VERSION(s): 2.3.1 DESCRIPTION: PyTables(tables) is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data |
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python VERSION(s): 2.5.1 2.5.5 2.6.4 2.7.2 3.1.1 DESCRIPTION: python is a programming language that lets you work more quickly and integrate your systems more effectively. |
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python VERSION(s): 2.6.7, 3.2.2 DESCRIPTION: python is a programming language that lets you work more quickly and integrate your systems more effectively. |
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Qhull VERSION(s): 2010.1 DESCRIPTION: Qhull is a general dimension convex hull program that reads a set of points from stdin, and outputs the smallest convex set that contains the points to stdout. |
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Qiime VERSION(s): 1.4.0 DESCRIPTION: QIIME (canonically pronounced 'Chime') stands for "Quantitative Insights Into Microbial Ecology'. It allows a range of community analyses suitable for microbiome data using traditional and high-throughput sequencing methods. |
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Qt VERSION(s): 3.3.8 4.3.5 4.7.2 DESCRIPTION: Qt is a comprehensive cross-platform C++ application framework. |
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Quarc VERSION(s): 2011-05-09 DESCRIPTION: This package contains a couple of useful programs to analyse a set of short read data. |
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QuiMiCa VERSION(s): 0.99.35 DESCRIPTION: Quantum mechanics Monte Carlo simulation program |
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R VERSION(s): 2.7.2, 2.10.1, 2.12.0, 2.15.0 DESCRIPTION: Software environment for statistical computing and graphics |
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RAxML VERSION(s): 7.0.4 DESCRIPTION: A propgram for sequentila and parallel Maximum Likelihood based inference of large phylogenetic trees. |
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Ray VERSION(s): 2.0.0 DESCRIPTION: A computer-controlled software that performs parallel de novo genome assemblies of next-gen sequencing data using message passing interface. |
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Ray VERSION(s): 0.1.0 1.2.0 1.6.1 DESCRIPTION: A computer-controlled software that performs parallel de novo genome assemblies of next-gen sequencing data using message passing interface. |
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RELION VERSION(s): 1.0 DESCRIPTION: REgularised LIkelihood OptimisatioN is a computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. |
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RepeatMasker VERSION(s): 3.2.9 DESCRIPTION: RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. |
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Rmpi VERSION(s): 0.5-9 DESCRIPTION: R package that provides an interface to MPI for distributed parallel computing. |
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RNA-SeQC VERSION(s): 1.1.7 DESCRIPTION: RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. |
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RNV VERSION(s): 1.7.8 DESCRIPTION: RNV is an implementation of Relax NG Compact Syntax validator. It is written in ANSI C and the command-line utility uses Expat. |
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RSEM VERSION(s): DESCRIPTION: RNA-Seq by Expectation-Maximization |
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RSEQtools VERSION(s): 0.6 DESCRIPTION: A modular framework to analyze RNA-Seq data using compact and anonymized data summaries. |
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Ruby VERSION(s): 1.8.7 1.9.2 DESCRIPTION: A dynamic, open source programming language with a focus on simplicity and productivity. |
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SAMTools VERSION(s): r540, 0.1.8 (r613), 0.1.13, 0.1.16, 0.1.18 DESCRIPTION: Utilities for manipulating alignments in the SAM (sequence Alignment/Map) format, including sorting, merging, indexing and generating alignments in a per-position format. |
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sate VERSION(s): 2.1.0 DESCRIPTION: SATé is a software package for inferring a sequence alignment and phylogenetic tree. |
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schrodinger VERSION(s): 2009 2010 2011 DESCRIPTION: Schrödinger is an extensive software suite containing modules to perform various modelling tasks such as drug docking protein homology and also quantum mechanics. |
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SCIRun VERSION(s): 4.3 DESCRIPTION: A problem solving environment, for modeling, simulation and visualization of scientific problems |
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SCons VERSION(s): 2.0.0 DESCRIPTION: SCons is an Open Source software construction tool—that is, a next-generation build tool. |
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SCons VERSION(s): 2.0.1 DESCRIPTION: SCons is an Open Source software construction tool—that is, a next-generation build tool. |
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Seg3D VERSION(s): 1.12 DESCRIPTION: A volume segmentation and processing tool |
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segadapter VERSION(s): 1.2 DESCRIPTION: Provide an open source learning-based software that automatically learns how to transfer the output of a host segmentation tool closer to the user's manual segmentation using the image data and manual segmentation provided by the user. |
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Semtex VERSION(s): 6.1 DESCRIPTION: A family of spectral element simulation codes |
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Semtex VERSION(s): 2010 DESCRIPTION: A family of spectral element simulation codes |
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seqclean VERSION(s): 20120106 DESCRIPTION: a script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences. |
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seqgene VERSION(s): 2.5 DESCRIPTION: SeqGene is an open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, allele specific expression, and expression-genotying association analysis. |
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SGA VERSION(s): 0.9.17-8 DESCRIPTION: SGA is a de novo genome assembler based on the concept of string graphs. |
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SHRiMP VERSION(s): 2.0.1 2.1.1 2.2.1 DESCRIPTION: Aligning genomic reads against a atrget genome, particularly NGS sequences and Applied Biosystem's colourspace genomic representation |
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SIMLE VERSION(s): 120521 DESCRIPTION: Single-particle IMage Processing Linux Engine (SIMPLE) does ab initio 3D reconstruction (programs cluster & origami), heterogeneity analysis (programs cluster, origami & cycler), and high-resolution refinement (programs align, reconstruct, automask & cycler) |
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SLEPc VERSION(s): 3.1-p6 DESCRIPTION: SLEPc, the Scalable Library for Eigenvalue Problem Computations, is a software package for the solution of large sparse eigenvalue problems on parallel computers. |
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SNOW VERSION(s): 0.3 DESCRIPTION: R package that allows R to run on a Simple Network of Workstations |
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Snowfall VERSION(s): 1.61 DESCRIPTION: R package that allows R to run on a Simple Netwrok of Workstations by extending SNOW. |
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snpEff VERSION(s): 1.9.5 2.0.5d DESCRIPTION: Variant effect predictor tool |
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SNVMix2 VERSION(s): 0.11.8-r4 DESCRIPTION: The script SNVMix2_threshold_select.pl automates parameter training and threshold selection with the models described in Goya et al, 2010 |
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SOAPdenovo VERSION(s): 1.04, 1.05 DESCRIPTION: Short-read denovo assembly. |
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Somatic Sniper VERSION(s): 1.0.0 DESCRIPTION: The purpose of this program is to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two bam files). |
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SPAdes VERSION(s): 2.4.0 DESCRIPTION: SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. |
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SparseHash VERSION(s): 1.7 DESCRIPTION: The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. |
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spider VERSION(s): 18.15 19.00 DESCRIPTION: Image processing system for electron microscopy. |
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spider VERSION(s): 18.15 DESCRIPTION: Image processing system for electron microscopy. |
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spire VERSION(s): 1.5.4 DESCRIPTION: Spire is designed to simplify running projects that consist of numerous SPIDER batch files. |
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SRA Toolkit VERSION(s): 2.1.16 DESCRIPTION: The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives |
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SRMA VERSION(s): 0.1.7 DESCRIPTION: Short read micro re-aligner |
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SSAHA2 VERSION(s): 2.5.2 DESCRIPTION: Pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. |
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SSPACE_Basic VERSION(s): 2.0 DESCRIPTION: SSPACE is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired-end libraries, or even a combination. |
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Structure VERSION(s): 2.3.2.1 DESCRIPTION: The program structure is a free software package for using multi-locus genotype data to investigate population structure. |
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SVDetect VERSION(s): r0.7m DESCRIPTION: SVDetect - Program designed to the detection of structural variations from paired-ends data |
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tabix VERSION(s): 0.2.5 DESCRIPTION: Generic indexer for TAB-delimited genome position files. |
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TCL VERSION(s): 8.5.8 8.5.10 DESCRIPTION: Tool Command Language |
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TCL VERSION(s): 8.3.3 DESCRIPTION: Tool Command Language |
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textir VERSION(s): 0.5 DESCRIPTION: A fast text document retrieval engine |
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TGICL VERSION(s): 2.1 DESCRIPTION: The purpose of this package is to efficiently cluster and create assemblies (contigs) from a set of DNA sequences given in a fasta file. |
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Tinker VERSION(s): 5.1.05 DESCRIPTION: Software tools for molecular design |
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tmap VERSION(s): 0.1.3; 0.3.7 DESCRIPTION: DNA sequence aligner for Ion Torrent data |
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TopHat VERSION(s): 1.3.0 DESCRIPTION: A spliced read mapper for RNA-Seq |
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TrackVis VERSION(s): 0.5.1 DESCRIPTION: TrackVis is a software tool that can visualize and analyze fiber track data from diffusion MR imaging |
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Trinity VERSION(s): 03122011, 20120125p1, 20120608 DESCRIPTION: Process large volumes of RNA-Seq reads |
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unixODBC VERSION(s): 2.3.1 DESCRIPTION: Unix Open Database Connectivity |
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Valgrind VERSION(s): 3.5.0 3.6.1 DESCRIPTION: Valgrind is an instrumentation framework for building dynamic analysis tools. |
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Valgrind VERSION(s): 3.6.0 DESCRIPTION: Valgrind is an instrumentation framework for building dynamic analysis tools. |
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varscan VERSION(s): 2.2.11 DESCRIPTION: VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, IonTorrent, Roche/454, and similar instruments. |
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vcfCodingSnps VERSION(s): 1.5 DESCRIPTION: vcfCodingSnps is a SNP annotation tool that annotates coding variants in VCF files. |
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vcftools VERSION(s): 0.1.6, 0.1.8a, 0.1.9 DESCRIPTION: A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project |
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Velvet VERSION(s): 0.7.60, 1.0.13, 1.1.04, 1.1.05, 1.1.07, 1.2.07, 1.2.08 DESCRIPTION: Sequence assembler for very short reads |
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VelvetOptimiser VERSION(s): 2.1.8, 2.2.2, 2.2.4, 2.2.5 DESCRIPTION: VelvetOptimiser is a multi-threaded Perl script for automatically optimising the parameter options for the Velvet de novo sequence assembler. |
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VMD VERSION(s): 1.8.7; 1.9beta2; 1.9.1 DESCRIPTION: Visual Molecular Dynamics |
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VTK VERSION(s): 5.4.2 5.6.0 DESCRIPTION: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. |
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VTK VERSION(s): 5.6.1 DESCRIPTION: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. |
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VXL VERSION(s): 1.14.0 DESCRIPTION: C++ libraries for computer vision |
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web VERSION(s): 19.00 DESCRIPTION: Web is a graphical user interface for displaying and interacting with SPIDER format images. |
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wmake VERSION(s): 1.6 DESCRIPTION: wmake is called from the Allwmake scripts during the initial build of the complete OpenFOAM project but can be executed directly to update the compilation of any of the OpenFOAM components: |
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Xapian VERSION(s): 1.2.7 DESCRIPTION: Xapian is an Open Source Search Engine Library, released under the GPL. It's written in C++, with bindings to allow use from Perl, Python, PHP, Java, Tcl, C#, Ruby and Lua (so far!) |
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xerces VERSION(s): 2.8.0 DESCRIPTION: The Apache Xerces Project currently consists of the following sub-projects, each focused on the development of XML parsers and related components in various languages |
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Xmipp VERSION(s): 2.4 DESCRIPTION: Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy. |
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Xmipp VERSION(s): 2.4 DESCRIPTION: Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy. |
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xmlrpc-c VERSION(s): 1.06.41 DESCRIPTION: XML-RPC for C/C++ is a software package of programming libraries to help a C or C++ program use XML-RPC. |
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XSD VERSION(s): 3.3.0 DESCRIPTION: The XSD runtime library and generated code depend on existing libraries for XML parsing. |
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yasm VERSION(s): 1.1.0 DESCRIPTION: Yasm is a complete rewrite of the NASM assembler |
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zlib VERSION(s): 1.2.5 DESCRIPTION: zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. |
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zope VERSION(s): 3.4.0 DESCRIPTION: Zope is a Python-based application server for building secure and highly scalable web applications. |
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