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mrfast

mrFAST is a read mapper that is designed to map short reads to reference genome

Versions:2.6.1.0
License:GPLv3
Categories:bioinformatics
mricron

Image viewer for NIfTI images and DICOM conversion

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

mrsFAST is designed to map short reads to reference genome assemblies in a fast and memory-efficient manner.

Versions:3.4.0
License:GPLv3
Categories:bioinformatics
mrtrix

MRtrix provides a set of tools to perform various advanced diffusion MRI analyses.

Versions:3.0_RC3; 3.0_RC2
License:Mozill Public License, http://mozilla.org/MPL/2.0/
Categories:diffusion-weighted MRI, fMRI, neuroimaging, tractography
mummer

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.

Versions:3.23
License:GPLv2
Categories:bioinformatics
mummer4

MUMmer is a system for rapidly aligning large DNA sequences to one another.

Versions:4.0.0beta2
License:open source with citation: https://mummer4.github.io/
Categories:allignment, bioinformatics
murasaki

Murasaki produces anchors across genomes

Versions:1.68.6
License:GPL
Categories:bioinformatics
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

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] NAGWARE – f95/f90 fortran compiler

Versions:6.2-6214; 6.1-6120
License:fortran, compiler
Categories:
nanopolish

nanopolish is Signal-level algorithms for MinION data

Versions:0.9.2
License:MIT
Categories:Genomics, bioinformatics
nastran-research

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] Nastran is a multidisciplinary structural analysis application.

Versions:2017.1
License:Non-commercial research
Categories:FEA, structural analysis
ncbi-blast

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

Versions:2.5.0; 2.9.0; 2.2.29
License:United States Government Work under the terms of the United States Copyright Act
Categories:bioinformatics
ncbi-blast+

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

Versions:2.2.31
License:United States Government Work under the terms of the United States Copyright Act
Categories:bioinformatics
ncbi-vdb

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

Versions:2.8.2
License:GPLv2
Categories:bioinformatics
ncl

NCAR command language for visualization.

Versions:6.3.0; 6.4.0; 6.6.2
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:4.6.7; 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/14.0.2; 4.4.1 with intel/16.0.3; 4.4.1 with intel/17.0.1; 4.4.1 with pgi/16.4
Categories:Core, Development, library
netcdf-par

Libraries for creating and manipulating NetCDF files.

Versions:4.6.1 with impi/2017.1.132
Categories:Core, Development, library
netcdff-par

Libraries for creating and manipulating NetCDF files.

Versions:4.4.4 with impi/2017.1.132
Categories:Core, Development, library
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:None available
Categories:Math, Networking, 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
neuron

NEURON is a simulation environment for modeling individual neurons and networks of neurons.

Versions:7.5; 7.4; 7.3
License:GNU GPL
Categories:Neuron, simulation
ngs-sdk

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

Versions:2.8.2; 1.2.5
License:GPLv2
Categories:bioinformatics
ninja

Low-level build tool.

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

NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.

Versions:2.4.2
License:LGPL and MIT License
Categories:Nonlinear, Optimization, library
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; 6.8.0 with gcc/7.2.0 openmpi/3.0.0
Categories:
oclust

Pipeline for clustering long 16S rRNA sequencing reads, or any sequences, into Operational Taxonomic Units.

Versions:1.0.0
License:GPLv2
Categories:bioinformatics
octave

GNU Octave mathematics-oriented syntax with built-in plotting and visualization tools.

Versions:5.1.0
License:https://www.gnu.org/software/octave/license.html
Categories:Math, Visualization, plotting
oma

The OMA (“Orthologous MAtrix””) project is a method and database for the inference of orthologs among complete genomes.”

Versions:2.2.0
License:MPL 2.0
Categories:Genomics, Orthologs, bioinformatics
openblas

BLAS provides standard interfaces for linear algebra, including BLAS1 (vector-vector operations), BLAS2 (matrix-vector operations), and BLAS3 (matrix-matrix operations).

Versions:0.2.18
License:https://opensource.org/licenses/BSD-3-Clause
Categories:C++, Programming, library
opencv

OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.

Versions:2.4.13; 3.1.0; 3.2.0
License:http://opencv.org/
Categories:computer vision, machine learning
opencv-python

This module sets up PYTHONPATH for python-anaconda to use OpenCV.

Versions:2; 3
License:N/A
Categories:python
openfoam

OpenFOAM is a free, open source CFD software.

Versions:3.0+dev20160616; old-1.6-ext-07122012; 2.4.0; v1712; 3.0+
License:http://www.openfoam.com/documentation/licencing.php
Categories:CFD
openmpi

OpenMPI implementation of the MPI protocol

Versions:1.8.8 with gcc/4.8.5; 1.8.8 with intel/14.0.2; 3.0.0 with gcc/7.2.0; 3.0.0 with gcc/5.4.0; 3.0.0 with intel/18.0.1; 3.0.0 with intel/17.0.1; 1.6.5 with gcc/4.8.5; 1.6.5 with intel/14.0.2; 1.10.7 with gcc/7.2.0; 1.10.7 with pgi/19.1; 1.10.2 with gcc/4.8.5; 1.10.2 with gcc/4.9.3; 1.10.2 with gcc/5.4.0; 1.10.2 with intel/14.0.2-hwloc; 1.10.2 with intel/14.0.2; 1.10.2 with intel/16.0.3; 1.10.2 with intel/17.0.1; 1.10.2 with pgi/16.4; 3.0.1 with intel/17.0.1; 2.0.4 with gcc/4.8.5; 1.8.3 with intel/16.0.3
License:https://www.open-mpi.org/community/license.php
Categories:Core, Development, Utility
openmx

OpenMX is a nano-scale materal simulations package

Versions:3.8
License:GPLv2
Categories:DFT, Electronic Struture, materials
orange

Orange is a component-based data mining software. It includes a range of data visualization, exploration, preprocessing and modeling techniques.

Versions:3.0
License:http://orange.biolab.si/license/
Categories:Programming, library, python
orca

An ab initio, DFT and semiempirical SCF-MO package

Versions:4.0.1.2 with gcc/4.8.5
License:Free to acedemia with citation, see manual below
Categories:Materials Sciences
Current page: 8
Total pages: 13
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