| A++/P++ |
A++ and P++ are both C++ array class libraries, providing the user with array objects
to simplify the development of serial and parallel numerical codes.
|
| A5pipeline |
A5 is a pipeline for assembling DNA sequence data generated on the Illumina sequencing
platform. This README will take you through the steps necessary for running A5. |
| ACML 4.4.0, 5.0.0 |
ACML provides a free set of thoroughly optimized and threaded math routines for HPC,
scientific, engineering and related compute-intensive applications. ACML is ideal
for weather modeling, computational fluid dynamics, financial analysis, oil and gas
applications and more.
|
| ADINA 8.7 |
The ADINA System offers a one-system program for comprehensive finite element analyses
of structures, fluids, heat transfer, electromagnetics and multiphysics.
|
| Amber 11 |
"Amber" refers to two things: a set of molecular mechanical force fields for the simulation
of biomolecules (which are in the public domain, and are used in a variety of simulation
programs); and a package of molecular simulation programs which includes source code
and demos.
|
| ampliconnoise-1.25 |
AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced
PCR amplicons. It involves two steps: the removal of noise from the sequencing itself
and the removal of PCR point errors.
|
| AUTO-07p |
AUTO is a software for continuation and bifurcation problems in ordinary differential
equations
|
| autostem |
calculate high resolution (atomic or near atomic) conventional and scanning transmission
electron microscope (CTEM and STEM) images of thin specimens from first principles
using the multislice method for electrons (with simplifying assumptions for the interactive
versions) in the energy range of approximately 100 keV to 1OOO keV.
|
| BEAGLE |
an application programming interface (API) and library for high-performance statistical
phylogenetic inference - See more at: http://gpuscience.com/articles/beagle-an-application-programming-interface-and-hpc-library-for-statistical-phylogenetics/#sthash.VLcZRaIV.dpuf
|
| BEAST 1.6.1 |
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences.
It is entirely orientated towards rooted, time-measured phylogenies inferred using
strict or relaxed molecular clock models
|
| Bioconductor |
Bioconductor provides tools for the analysis and comprehension of high-throughput
genomic data. Bioconductor uses the R statistical programming language, and is open
source and open development.
|
| biom-format-0.9.3 |
The BIOM format is designed for general use in broad areas of comparative -omics.
For example, in marker-gene surveys, the primary use of this format is to represent
OTU tables: the observations in this case are OTUs and the matrix contains counts
corresponding to the number of times each OTU is observed in each sample.
|
| Biopython |
Biopython is a set of freely available tools for biological computation written in
Python by an international team of developers. It is a distributed collaborative effort
to develop Python libraries and applications which address the needs of current and
future work in bioinformatics.
|
| blast 2.2.25/.26/.28 |
Basic Local Alignment Search Tool is a sequence comparison algorithm optimized for
speed used to search sequence databases for optimal local alignments to a query.
|
| BLAT 3.5 |
BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of
length 25 bases or more. It may miss more divergent or shorter sequence alignments.
It will find perfect sequence matches of 20 bases. BLAT on proteins finds sequences
of 80% and greater similarity of length 20 amino acids or more.
|
| boost 1.53 |
Boost provides free peer-reviewed portable C++ source libraries. |
| Bowtie 0.12.9/2.0.6 |
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences
(reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie
indexes the genome with a Burrows-Wheeler index to keep its memory footprint small:
typically about 2.2 GB for the human genome (2.9 GB for paired-end).
|
| BWA 0.7.0 |
BWA is a program for aligning sequencing reads against a large reference genome (e.g.
human genome). It has two major components, one for read shorter than 150bp and the
other for longer reads.
|
| cdbtools-10.11.2010-release |
CDB (Constant DataBase) indexing and retrieval tools for multi-FASTA files |
| cdhit-3.1-release |
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide
sequences.CD-HIT is very fast and can handle extremely large databases. CD-HIT helps
to significantly reduce the computational and manual efforts in many sequence analysis
tasks and aids in understanding the data structure and correct the bias within a dataset.
|
| chimeraslayer-4.29.2010-release |
Chimera Slayer involves the following series of steps that operate to flag chimeric
16S rRNA sequences: (A) the ends of a query sequence are searched against an included
database of reference chimera-free 16S sequences to identify potential parents of
a chimera; (B) candidate parents of a chimera are selected as those that form a branched
best scoring alignment to the NAST-formatted query sequence; the NAST alignment of
the query sequence is improved in a ‘chimera-aware’ profile-based NAST realignment
to the selected reference parent sequences; and (D) an evolutionary framework is used
to flag query sequences found to exhibit greater sequence homology to an in silico
chimera formed between any two of the selected reference parent sequences.
|
| clearcut-1.0.9-release |
Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ) |
| Clustal W 2.1 |
Clustal W is a general purpose multiple alignment program for DNA or proteins. |
| Cogent |
Cogent is a toolkit for statistical analysis of biological sequences. |
| COMSOL 4.3 |
COMSOL Multiphysics is a finite element analysis, solver and Simulation software /
FEA Software package for various physics and engineering applications, especially
coupled phenomena, or multiphysics. COMSOL Multiphysics also offers an extensive interface
to MATLAB and its toolboxes for a large variety of programming, preprocessing and
postprocessing possibilities.
|
| CUDA 4.2, 5 |
CUDA (aka Compute Unified Device Architecture) is a parallel computing platform and
programming model created by NVIDIA and implemented by the graphics processing units
(GPUs) that they produce
|
| CULA R11, R14, sparse |
CULA™ is an implementation of the Linear Algebra PACK-age (LAPACK) interface for CUDA™-enabled
NVIDIA® graphics processing units (GPUs).
|
| cytoscape-2.7.0-release |
Cytoscape is an open source software platform for visualizing complex networks and
integrating these with any type of attribute data.
|
| delft3d 4.0, 5.0 |
Delft3D is a world leading 3D modeling suite to investigate hydrodynamics, sediment
transport and morphology and water quality for fluvial, estuarine and coastal environments.
|
| drisee-1.2-release |
DRISEE is a tool that utilizes artifactual duplicate reads (ADRs) to provide a platform
independent assessment of sequencing error in metagenomic (or genomic) sequencing
data. DRISEE is designed to consider shotgun data.
|
| exonerate 2.2 |
exonerate is a generic tool for pairwise sequence comparison.It allows you to align
sequences using a many alignment models, using either exhaustive dynamic programming,
or a variety of heuristics.
|
| FastTree |
FastTree is open-source software that infers approximately-maximum-likelihood phylogenetic
trees from alignments of nucleotide or protein sequences. FastTree can handle alignments
with up to a million of sequences in a reasonable amount of time and memory. For large
alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.
|
| fftw 2.1.5, 3.2.2, 3.3 |
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
in one or more dimensions, of arbitrary input size, and of both real and complex data
(as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
|
| gaussian 09 |
Starting from the fundamental laws of quantum mechanics, Gaussian 09 predicts the
energies, molecular structures, vibrational frequencies and molecular properties of
molecules and reactions in a wide variety of chemical environments.
|
| GCC 4.5.3, 4.6.2, 4.7.0, 4.7.1 |
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran,
Java, Ada, and Go, as well as libraries for these languages (libstdc++, libgcj,...).
|
| gg_otus-4feb2011-release |
GreenGenes OTU picker module for Qiime |
| Globus 5.2.3 |
The open source Globus® Toolkit is a fundamental enabling technology for the "Grid,"
letting people share computing power, databases, and other tools securely online across
corporate, institutional, and geographic boundaries without sacrificing local autonomy.
|
| glpk 4.4.5 |
The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale
linear programming (LP), mixed integer programming (MIP), and other related problems.
It is a set of routines written in ANSI C and organized in the form of a callable
library.
|
| GMAC 1.1.1 |
GMAC is a user-level library that implements an Asymmetric Distributed Shared Memory
model to be used by CUDA programs. An ADSM model allows CPU code to access data hosted
in accelerator (GPU) memory.
|
| gmp 4.3.2 |
GMP is a free library for arbitrary precision arithmetic, operating on signed integers,
rational numbers, and floating point numbers. There is no practical limit to the precision
except the ones implied by the available memory in the machine GMP runs on. GMP has
a rich set of functions, and the functions have a regular interface.
|
| GPUmat4 |
GPUmat allows standard MATLAB code to run on GPUs. The engine is written in C/C++
and based on NVIDIA CUDA.
|
| gromacs 4.6.1, 4.6.3, 5.0 |
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian
equations of motion for systems with hundreds to millions of particles. It is primarily
designed for biochemical molecules like proteins, lipids and nucleic acids that have
a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating
the nonbonded interactions (that usually dominate simulations) many groups are also
using it for research on non-biological systems, e.g. polymers.
|
| hdf5 1.8.4, 1.8.6 |
HDF5 is a data model, library, and file format for storing and managing data. It supports
an unlimited variety of datatypes, and is designed for flexible and efficient I/O
and for high volume and complex data.
|
| IDBA_UD |
IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data
with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. |
| IMa2 8.27.12 |
an implementation of the MCMC method for the analysis of genetic data under the Isolation
with Migration model of population divergence. IMa2 applies this model to genetic
data drawn from a pair of closely related populations or species. The results are
estimates of the marginal posterior probability densities for each of the model parameters.
|
| infernal-1.0.2-release |
Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for
RNA structure and sequence similarities. It is an implementation of a special case
of profile stochastic context-free grammars called covariance models (CMs). |
| Intel compiler 11.1-059, 11.1-072, 12.1.5, 13.0.1, 13.1.0 |
The Intel® Composer XE suites are available in several configurations that combine
industry leading C, C++ and Fortran compilers, programming models including Intel®
Cilk™ Plus and OpenMP*, performance libraries including Intel® Math Kernel Library
(Intel® MKL), Intel® Integrated Performance Primitives (Intel® IPP) and Intel® Threading
Building Blocks (Intel® TBB) for leadership application performance on systems using
Intel® Core™ and Xeon® processors, Intel® Xeon Phi™ coprocessors and compatible processors.
|
| Intel Memory Configuration Tool |
This application assists in finding optimal memory configurations for Intel ® Xeon
® Processor series platforms.
|
| iPython |
Python is an easy to learn, powerful programming language. It has efficient high-level
data structures and a simple but effective approach to object-oriented programming.
Python’s elegant syntax and dynamic typing, together with its interpreted nature,
make it an ideal language for scripting and rapid application development in many
areas on most platforms.The Python interpreter and the extensive standard library
are freely available in source or binary form for all major platforms from the Python
Web site, http://www.python.org/, and may be freely distributed. The same site also contains distributions of and
pointers to many free third party Python modules, programs and tools, and additional
documentation.
|
| Java developer kit 1.6, 1.7 |
For Java Developers. Includes a complete JRE plus tools for developing, debugging,
and monitoring Java applications.
|
| jinja2 |
Jinja2 is a template engine written in pure Python. It provides a Django inspired
non-XML syntax but supports inline expressions and an optional sandboxed environment.
|
| LAMMPS |
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular
Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules,
polymers) and solid-state materials (metals, semiconductors) and coarse-grained or
mesoscopic systems. It can be used to model atoms or, more generically, as a parallel
particle simulator at the atomic, meso, or continuum scale.
|
| libjacket 1.1 |
a broad and fast C/C++ library for GPU computing. With over 500 C/C++ functions, LIBJACKET
represents the largest GPU computing library in the world. This CUDA-based library
integrates seamlessly in any application enabling optimized utilization of NVIDIA
CUDA-capable GPUs, including powerful Tesla compute devices.
|
| libsvm 3.0 |
LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression
(epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class
classification. |
| magma 1.0.0 |
MAGMA provides implementations for CUDA, OpenCL, and Intel Xeon Phi. |
| MaSuRCA 2.0.0 |
MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn
graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets
containing only short reads from Illumina sequencing or a mixture of short reads and
long reads
|
| matlab R2008b, R2010b, R1011a, R2012a |
MATLAB® is a high-level language and interactive environment for numerical computation, visualization,
and programming. Using MATLAB, you can analyze data, develop algorithms, and create
models and applications. |
| MatStudio 5.0.1 |
Materials Studio is a complete modeling and simulation environment designed to allow
researchers in materials science and chemistry to predict and understand the relationships
of a material’s atomic and molecular structure with its properties and behavior.
|
| metis 4.0 |
METIS is a set of serial programs for partitioning graphs, partitioning finite element
meshes, and producing fill reducing orderings for sparse matrices.
|
| molden |
Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK
, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports
a number of other programs via the Molden Format. Molden reads all the required information
from the GAMESS / GAUSSIAN outputfile. Molden is capable of displaying Molecular Orbitals,
the electron density and the Molecular minus Atomic density.
|
| mothur 1.29 |
This project seeks to develop a single piece of open-source, expandable software to
fill the bioinformatics needs of the microbial ecology community. It has incorporated
the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more.
In addition to improving the flexibility of these algorithms, they have added a number
of other features including calculators and visualization tools.
|
| mpi4py |
Provides bindings of the Message Passing Interface (MPI) standard for the Python programming
language, allowing any Python program to exploit multiple processors.
|
| mpiBLAST 1.6 |
mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST.
By efficiently utilizing distributed computational resources through database fragmentation,
query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI
BLAST performance by several orders of magnitude while scaling to hundreds of processors.
|
| mpiCH2 |
MPICH2 is an implementation of the Message-Passing Interface (MPI). The goals of MPICH2
are to provide an MPI implementation for important platforms, including clusters,
SMPs, and massively parallel processors. It also provides a vehicle for MPI implementation
research and for developing new and better parallel programming environments.
|
| mpqc 2.3.1 |
MPQC is the Massively Parallel Quantum Chemistry Program. It computes properties of
atoms and molecules from first principles using the time independent Schrödinger equation.
It runs on a wide range of architectures ranging from single many-core computers to
massively parallel computers. Its design is object oriented, using the C++ programming
language.
|
| mrbayes 3.1.2, 3.2 |
MrBayes is a program for Bayesian inference and model choice across a wide range of
phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC)
methods to estimate the posterior distribution of model parameters.
|
| MSAProbs |
MSAProbs is a new and practical multiple alignment algorithm for protein sequences.
The design of MSAProbs is based on a combination of pair hidden Markov models and
partition functions to calculate posterior probabilities.
|
| muscle-3.8.31-release |
MUSCLE is one of the best-performing multiple alignment programs according to published
benchmark tests, with accuracy and speed that are consistently better than CLUSTALW.
MUSCLE can align hundreds of sequences in seconds.
|
| mvapich2 |
MVAPICH2 (MPI-3 over InfiniBand) is an MPI-3 implementation based on MPICH ADI3 layer. |
| NAMD 2.83, 2.9 |
a parallel molecular dynamics code designed for high-performance simulation of large
biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of
processors on high-end parallel platforms and tens of processors on commodity clusters
using gigabit ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR
|
| netcdf 3.6.3, 4.1.1 |
NetCDF is a set of software libraries and self-describing, machine-independent data
formats that support the creation, access, and sharing of array-oriented scientific
data.
|
| Numpy |
NumPy is the fundamental package for scientific computing with Python. It contains
among other things: a powerful N-dimensional array object, sophisticated (broadcasting)
functions, tools for integrating C/C++ and Fortran code, and useful linear algebra,
Fourier transform, and random number capabilities. Besides its obvious scientific
uses, NumPy can also be used as an efficient multi-dimensional container of generic
data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily
integrate with a wide variety of databases.
|
| nwchem 6.0 |
NWChem aims to provide its users with computational chemistry tools that are scalable
both in their ability to treat large scientific computational chemistry problems efficiently,
and in their use of available parallel computing resources from high-performance parallel
supercomputers to conventional workstation clusters.
|
| octave 3.2.4 |
GNU Octave is a high-level interpreted language, primarily intended for numerical
computations. It provides capabilities for the numerical solution of linear and nonlinear
problems, and for performing other numerical experiments. It also provides extensive
graphics capabilities for data visualization and manipulation. Octave is normally
used through its interactive command line interface, but it can also be used to write
non-interactive programs. The Octave language is quite similar to Matlab so that most
programs are easily portable.
|
| open64 4.2.2.2 |
Open64 has been well-recognized as an industrial-strength production compiler. It
is the final result of research contributions from a number of compiler groups around
the world. Formerly known as Pro64, Open64 was initially created by SGI from SGI's
MIPSPro compiler, and licensed under the GNU Public License (GPL v2).
|
| opencurrent 1.1 |
OpenCurrent is an open source C++ library for solving Partial Differential Equations
(PDEs) over regular grids using the CUDA platform from NVIDIA.
|
| openFOAM 2.1.1 |
OpenFOAM is first and foremost a C++ library, used primarily to create executables,
known as applications. The applications fall into two categories: solvers, that are
each designed to solve a specific problem in continuum mechanics; and utilities, that
are designed to perform tasks that involve data manipulation.
|
| openMM 3.1.1 |
OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone
application for running simulations, or as a library you call from your own code.
Itprovides a combination of extreme flexibility (through custom forces and integrators),
openness, and high performance (especially on recent GPUs) that make it truly unique
among simulation codes.
|
| openmpi 1.6.1 |
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. Open MPI
is therefore able to combine the expertise, technologies, and resources from all across
the High Performance Computing community in order to build the best MPI library available.
Open MPI offers advantages for system and software vendors, application developers
and computer science researchers.
|
| Pandaseq |
PANDAseq assembles paired-end reads rapidly and with the correction of most errors.
Uncertain error corrections come from reads with many low-quality bases identified
by upstream processing.
|
| paraview 3.12 |
ParaView is an open-source, multi-platform data analysis and visualization application.
ParaView users can quickly build visualizations to analyze their data using qualitative
and quantitative techniques. The data ParaView was developed to analyze extremely
large datasets using distributed memory computing resources. It can be run on supercomputers
to analyze datasets of terascale as well as on laptops for smaller data exploration
can be done interactively in 3D or programmatically using ParaView's batch processing
capabilities.
|
| parsinsert-1.0.4-release |
ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification
for sequences for microbial community sequence analysis.
|
| pgi 12.9 |
PGI® Workstation: PGI's suite of compilers and toolsPGI Workstation™ is PGI's single-user
scientific and engineering compilers and tools product.
|
| pplacer-1.1-release |
Pplacer places query sequences on a fixed reference phylogenetic tree to maximize
phylogenetic likelihood or posterior probability according to a reference alignment.
|
| pprospector-1.0.1-release |
Primer Prospector is a pipeline of programs to design and analyze PCR primers. |
| prottest 3.2 |
ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid
replacement for the data at hand. ProtTest makes this selection by finding the model
in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian
Information Criterion (BIC) score or Decision Theory Criterion (DT). At the same time,
ProtTest obtains model-averaged estimates of different parameters (including a model-averaged
phylogenetic tree) and calculates their importance(Posada and Buckley 2004). ProtTest
differs from its nucleotide analog jModeltest (Posada 2008) in that it does not include
likelihood ratio tests, as not all models included in ProtTest are nested.
|
| Pygments |
Pygments is a generic syntax highlighter for general use in all kinds of software
such as forum systems, wikis or other applications that need to prettify source code.
|
| Pynast |
PyNAST is a reimplementation of NAST, introducing new features that increase its portability
and flexibility. Its availability as an open source application with three convenient
interfaces will allow the application of the NAST algorithm on a wider basis, to larger
datasets, and in novel domains.
|
| Python 2.7.2, 2.7.3, 2.7.5, 3.2.1, 3.2.3 |
Python is a remarkably powerful dynamic programming language that is used in a wide
variety of application domains. Python is often compared to Tcl, Perl, Ruby, Scheme
or Java.
|
| Pytz |
PyTZ is a Python library that allows cross-platform and accurate timezone calculations. |
| Pyzmq |
Pyzmq provides python bindings for ØMQ and allows you to leverage ØMQ in python applications. |
| qchem 4.0, 4.0.1 |
Q-Chem is a comprehensive ab initio quantum chemistry package for accurate predictions
of molecular structures, reactivities, and vibrational, electronic and NMR spectra.
The new release of Q-Chem 4 represents the state-of-the-art of methodology from the
highest performance DFT/HF calculations to high level post-HF correlation methods:
|
| qhull |
Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace
intersection about a point, furthest-site Delaunay triangulation, and furthest-site
Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull
implements the Quickhull algorithm for computing the convex hull. It handles roundoff
errors from floating point arithmetic. It computes volumes, surface areas, and approximations
to the convex hull.
|
| Qiime |
QIIME is an open source software package for comparison and analysis of microbial
communities, primarily based on high-throughput amplicon sequencing data (such as
SSU rRNA) generated on a variety of platforms, but also supporting analysis of other
types of data (such as shotgun metagenomic data).
|
| qrupdate |
Library for updating of QR and Cholesky decompositions |
| quantum espresso 4.3.2, 5.0.2 |
An integrated suite of Open-Source computer codes for electronic-structure calculations
and materials modeling at the nanoscale. It is based on density-functional theory,
plane waves, and pseudopotentials.
|
| QUAST 2.2 |
QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. |
| r-2.151, 3.0.1 |
R is a system for statistical computation and graphics. It consists of a language
plus a run-time environment with graphics, a debugger, access to certain system functions,
and the ability to run programs stored in script files. a
|
| raxml-7.3.0-release |
RAxML is a fast implementation of maximum-likelihood (ML) phylogeny estimation that
operates on both nucleotide and protein sequence alignments.
|
| rdpclassifier-2.2-release |
The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately
provides taxonomic assignments from domain to genus, with confidence estimates for
each assignment
|
| Roche 454 (2 versions) |
Analysis software for 454 Sequencing |
| rtax-0.981-release |
RTAX is specifically designed for assigning taxonomy to paired-end reads, but additionally
works on single-end reads
|
| SOAPdenovo 2.04 |
SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly
for the human-sized genomes. The program is specially designed to assemble Illumina
GA short reads. It creates new opportunities for building reference sequences and
carrying out accurate analyses of unexplored genomes in a cost effective way.
|
| SPAdes 2.5.0 |
SPAdes – St. Petersburg genome assembler – is intended for both standard isolates
and single-cell MDA bacteria assemblies.
|
| sphinx-1.0.4-release |
Sphinx is a tool that makes it easy to create documentation for Python projects |
| SQLAlchemy-0.7.1-release |
SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives application
developers the full power and flexibility of SQL. It provides a full suite of well
known enterprise-level persistence patterns, designed for efficient and high-performing
database access, adapted into a simple and Pythonic domain language.
|
| suitesparse |
Mathematic packages for Matlab and Metis |
| sunstudio 12.1 |
Sun Studio software includes compilers, libraries, and tools for application development
in C, C++, and Fortran, on Solaris, OpenSolaris, and Linux systems, on SPARC and x86
platforms.
|
| terachem |
TeraChem is general purpose quantum chemistry software designed to run on NVIDIA GPU
architectures under a 64-bit Linux operating system.
|
| Tophat |
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads
to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie,
and then analyzes the mapping results to identify splice junctions between exons.
|
| Tornado |
Tornado is a Python web framework and asynchronous networking library |
| trilinos 11.0 |
The Trilinos Project is an effort to develop and implement robust algorithms and enabling
technologies using modern object-oriented software design, while still leveraging
the value of established libraries such as PETSc, Metis/ParMetis, SuperLU, Aztec,
the BLAS and LAPACK. It emphasizes abstract interfaces for maximum flexibility of
component interchanging, and provides a full-featured set of concrete classes that
implement all abstract interfaces.
|
| trinity |
Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem,
represents a novel method for the efficient and robust de novo reconstruction of transcriptomes
from RNA-seq data. Trinity combines three independent software modules: Inchworm,
Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq
reads. Trinity partitions the sequence data into many individual de Bruijn graphs,
each representing the transcriptional complexity at at a given gene or locus, and
then processes each graph independently to extract full-length splicing isoforms and
to tease apart transcripts derived from paralogous genes.
|
| turbomole |
TURBOMOLE has been designed for robust and fast quantum chemical applications. |
| uclust-1.2.22-release |
Extreme High-speed Sequence Clustering, Aligment and Database Search |
| vienna-1.8.4-release |
A package for RNA secondary structure prediction and comparison |
| visit 2.4.0, 2.5.2, 2.6.1 |
VisIt is a free interactive parallel visualization and graphical analysis tool for
viewing scientific data on Unix and PC platforms. Users can quickly generate visualizations
from their data, animate them through time, manipulate them, and save the resulting
images for presentations. VisIt contains a rich set of visualization features so that
you can view your data in a variety of ways. It can be used to visualize scalar and
vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured
meshes. VisIt was designed to handle very large data set sizes in the terascale range
and yet can also handle small data sets in the kilobyte range.
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| vmd 1.9 |
VMD incorporates many new improvements for high quality rendering and export of molecular
scenes, new analysis features, support for new molecular data file formats, and many
performance improvements. Many new and updated structure building and analysis tools
have been added in this release, easing the process of preparing, running, and analyzing
biomolecular simulations. This release also contains many performance and efficiency
improvements that are particiularly beneficial for modeling, visualizing, and analyzing
very large structures with up to 100 million atoms. VMD makes extensive use of multi-core
processors and GPU acceleration to speed up computationally demanding analysis and
visualization tasks including key structure and trajectory analysis features, interactive
molecular dynamics, and high-quality ray tracing of molecular scenes. VMD now takes
advantage of multiple GPUs for very fast display of molecular orbitals arising in
quantum chemistry calculations.
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| wolfram mathematica 8 |
Mathematica 8 introduces free-form linguistic input—a whole new way to compute. Enter
plain English; get immediate results—no syntax required. It's a new entry point into
the complete Mathematica workflow, now upgraded with 500 additional functions and
7 application areas—including the world's most advanced statistics capability and
state-of-the-art image processing.
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| zephyr 2.0.3 |
The current release of OpenMM Zephyr enables acceleration of molecular dynamics on
specific NVIDIA and ATI GPU cards and operating systems.
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| zmq |
ØMQ (also seen as ZeroMQ, 0MQ, zmq) looks like an embeddable networking library but
acts like a concurrency framework. It gives you sockets that carry atomic messages
across various transports like in-process, inter-process, TCP, and multicast. You
can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution,
and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous
I/O model gives you scalable multicore applications, built as asynchronous message-processing
tasks. It has a score of language APIs and runs on most operating systems. ØMQ is
from iMatix and is LGPLv3 open source.
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