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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:1.39.5; 1.39.0; 1.38.1; 1.40.2; 1.37.6; 1.39.3; 1.40.0; 1.37.1
License:GPLv3
Categories:bioinformatics
mpb

MIT Photonic-Bands (MPB) package is a free program for computing the band structures (dispersion relations) and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers.

Versions:1.5
License:http://ab-initio.mit.edu/wiki/index.php/MPB_License_and_Copyright
Categories:band structures, electronic structure
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
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
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:6.1-6120
License:fortran, compiler
Categories:
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; 2.2.29
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
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/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
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.

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
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:
oclust

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

Versions:1.0.0
License:GPLv2
Categories:bioinformatics
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; 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; 1.10.2 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; 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
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
orthofinder

Accurate inference of orthologous gene groups made easy.

Versions:2.1.2
License:GPL v3
Categories:bioinformatics
p4

P4 is a Python package for maximum likelihood and Bayesian analysis of molecular sequences.

Versions:201804
License:GPLv2
Categories:Bayesian, phylogenetics
p4vasp

This software is Open Source. p4VASP is a visualization suite for the Vienna Ab-initio Simulation Package (VASP).

Versions:0.3.29
License:http://www.p4vasp.at
Categories:crystal symmetries, electronic structure, vizualization
p7zip

p7zip is a port of 7za.exe, compression app, for POSIX systems like Unix.

Versions:15.14.1
License:http://www.7-zip.org/license.txt
Categories:7zip, archiver, archives, compression, zip
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