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maple

Maple is a symbolic mathematics program.

Versions:18
License:http://www.maplesoft.com/documentation_center/Maplesoft_EULA.pdf
Categories:mathematics
marge

Model-based Analysis of Regulation of Gene Expression

Versions:1.0
License:GPLv2
Categories:bioinformatics
masurca

MaSuRCA is whole genome assembly software.

Versions:2.3.2
License:GPLv2
Categories:bioinformatics
mathematica

Mathematical and technical computing package.

Versions:10.3.1
License:http://www.wolfram.com/legal/agreements/wolfram-mathematica.html
Categories:mathematics, symbolic algebra
matlab

Matlab programming environment.

Versions:R2016a
Categories:Programming, mathematics, simulation
maven

Maven is a software project management and comprehension tool

Versions:3.3.9
License:GPLv3
Categories:bioinformatics
mcl

MCL is a fast and scalable unsupervised cluster algorithm for graphs based on simulation of flow in graphs.

Versions:14-137; 14-137
License:GPLv3
Categories:bioinformatics
mcnp

MCNP is a Monte Carlo N-Particle code.

Versions:6.1
License:User provided
Categories:Nuclear, reactor
mcnpx

MCNP is a Monte Carlo N-Particle code.

Versions:2.7.0
License:User provided
Categories:Nuclear, reactor
meep

Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems, along with our MPB eigenmode package.

Versions:parallel; single
License:GPLv2 (or later)
Categories:FDTD, electromagnetic system modeling, finite-difference, simulation, time-domain
megahit

MEGAHIT is a single node assembler for large and complex metagenomics NGS reads

Versions:1.0.6
License:GPLv2
Categories:bioinformatics
meme

MEME discovers novel, ungapped motifs in your sequences

Versions:4.11.2
License:GPLv2
Categories:bioinformatics
metabat

MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities

Versions:0.32.4
Categories:Special Berkeley license
metaCRISPR

metaCRISPR is a tool to assemble CRISPRs

Versions:1.0.0
License:GPLv3
Categories:bioinformatics
metaxa2

Metaxa2: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data

Versions:2.1.3
License:GNU GPLv3
Categories:Metagenomics, bioinformatics
metis

METIS – Serial Graph Partitioning and Fill-reducing Matrix Ordering

Versions:5.1.0-intel-16.0.3
License:http://glaros.dtc.umn.edu/gkhome/metis/parmetis/download
Categories:matrices, matrix, ordering, partitioning
minced

MinCED – Mining CRISPRs in Environmental Datasets

Versions:0.2.0
License:GPLv2
Categories:bioinformatics
mkl

Intel optimized BLAS/LAPACK libraries, also including FFT and other mathematical and statistical routines.

Versions:11.3.3
License:https://software.intel.com/sites/default/files/managed/86/1d/Master_EULA_for_Intel_Sw_Development_Products.pdf
Categories:BLAS, Core, Development, LAPACK, library
mmseq

Transcript and gene level expression analysis using multi-mapping RNA-seq reads

Versions:1.0.9
License:https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html
Categories:Application, bioinformatics
molpro

Molpro is a comprehensive system of ab initio programs for advanced molecular electronic structure calculations.

Versions:2012.1
License:http://www.molpro.net/info/products.php?portal=visitor&choice=Licence+types
Categories:Molecular Electronic structure, Molecular structure, Quantum Chemistry
mothur

Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. It incorporates the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more.

Versions:1.38.1; 1.37.6; 1.37.1
License:GPLv3
Categories:bioinformatics
mpi4py-dev

MPI bindings for use within Python.

Versions:2.0.0
License:http://www.scipy.org/scipylib/license.html
Categories:MPI, Programming, python
mplayer

MPlayer is a movie player supporting many different video files and output drivers.

Versions:1.3.0
License:GNU GPL v2
Categories:Image, Player, audio, video
mrbayes

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.

Versions:3.2.6
License:GNU GPL v3 or later
Categories:Bayesian, MCMC, bioinformatics, phylogenetics
mricron

Image viewer for NIfTI images and DICOM conversion

Versions:30apr2016
License:Standard BSD 2-Clause license
Categories:DICOM, NIfTI, fMRI, neuroimaging
muscle

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. Most users learn everything they need to know about MUSCLE in a few minutes – only a handful of command-line options are needed to perform common alignment tasks.

Versions:3.8.31
License:Public Domain (http://www.drive5.com/muscle/manual/license.html)
Categories:Alignment, bioinformatics
nagf95

NAGWARE – f95/f90 fortran compiler

Versions:5.3.2; 6.1
License:fortran, compiler
Categories:
ncbi-blast

Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool.

Versions:2.2.29; 2.5.0
License:United States Government Work under the terms of the United States Copyright Act
Categories:bioinformatics
ncl

NCAR command language for visualization.

Versions:6.3.0
License:http://www2.ucar.edu/terms-of-use
Categories:HDF5, NetCDF, Visualization
nco

The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5.

Versions:4.6.1
License:GNU GPL v1.3 or later
Categories:NetCDF, Utilities
ncview

Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. It runs on UNIX platforms under X11, R4 or higher.

Versions:2.1.7
License:GNU GPL V3
Categories:NetCDF, Utility, visual browser
netcdf

Libraries for creating and manipulating NetCDF files.

Versions:4.4.1 with gcc/4.8.5; 4.4.1 with gcc/4.9.3; 4.4.1 with gcc/5.4.0; 4.4.1 with intel/16.0.3; 4.4.1 with intel/14.0.2; 4.4.1 with pgi/16.4
Categories:Core, Development, library
networkx

NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

Versions:1.9.1
Supplier documentation:http://google.com
ARC-TS documentation:http://google.com
License:http://google.com
Categories:;ython, network, numerical
Parent module:sph
networkx

NetworkX is a Python language software package for the creation, manipulation, and study of the structure, dynamics, and function of complex networks.

Versions:2.0-dev
License:Math, Networking, Library
Categories:
neuron

NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties.

Versions:7.4; 7.3
License:GNU GPL
Categories:Neurons
ngs-sdk

NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.

Versions:1.2.5
License:GPLv2
Categories:bioinformatics
ninja

Low-level build tool.

Versions:1.7.1
License:None provided
Categories:Programming, Utility, build system
nodejs

Node.js is an asynchronous event driven JavaScript runtime.

Versions:4.4.7
License:https://nodejs.org/en/about/
Categories:JavaScript
numpy-dev

Numerical libraries for use within Python.

Versions:1.11.1
License:http://www.numpy.org/license.html
Categories:BLAS, LAPACK, Programming, numerical library, python
nwchem

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.

Versions:6.6.0 with gcc/5.4.0 openmpi/1.10.2
Categories:
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