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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
metal

METAL is a tool for meta-analysis genomewide association scans.

Versions:20110325
License:GPLv2
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-17.0.1; 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
minorseq

Includes the utilities: juliet, cleric and fuse

Versions:1.0
License:GPLv2
Categories:bioinformatics
mira

Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data.

Versions:4.0.2
License:GPL2
Categories:bioinformatics sequencing assembler genome
mirdeep

PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics.

Versions:2.0.0.8
License:LGPL
Categories:Biostatistics, Perl, Script
mkl

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

Versions:11.1.2; 2017.0.1; 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; 1.1.0
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:1.39.5; 1.39.0; 1.38.1; 1.37.6; 1.39.3; 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_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:7.4; 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:
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Total pages: 10
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