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lapack

LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.

Versions:3.4.2
License:http://www.netlib.org/lapack/LICENSE.txt
Categories:libraries
latexdiff

Determine and mark up significant differences between LATEX files

Versions:1.2.0
License:GPLv2
Categories:bioinformatics
lenstool

A gravitational lensing software for modeling mass distribution of galaxies and clusters (strong and weak regime).

Versions:6.8.1; 7.0
License:Unknown, contact author jean-paul.kneib@lam.fr
Categories:Astronomy, Gravitation, gravitational lensing
libctl

Guile-based library implementing flexible control files for scientific simulations.

Versions:3.2.2
License:GPL
Categories:Utility, library
liftOver

liftOver converts genome coordinates between assemblies

Versions:1.0.0
License:GPLv3
Categories:bioinformatics
ls-bsr

Large Scale Blast Score Ratio

Versions:1.0
License:GPLv3
Categories:bioinformatics
lsdyna-coe

LS-DYNA finite element analysis software.

Versions:R6.1.0; R8.1.0
License:None provided
Categories:finite element, multiphysics, simulation
lsdyna-umtri

LS-DYNA finite element analysis software.

Versions:R6.1.0; R8.1.0; R8.1.0-exp
License:None provided
Categories:finite element, multiphysics, simulation
mach

MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

Versions:1.0.18
License:Math, Biostatistics, Application
Categories:
macs2

Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding sites.

Versions:2.1.0
License:GPLv2
Categories:bioinformatics
mafft

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc.

Versions:7.294
License:http://mafft.cbrc.jp/alignment/software/license66.txt
Categories:Alignment, bioinformatics
mageck

Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout

Versions:0.5.5; 0.5.6; 0.5.4
License:GPLv3
Categories:bioinformatics
maker

MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.

Versions:2.3.8; 2.31.8b-no-mpi; 2.31.8a; 2.31.8
License:Perl Foundation Artistic License 2.0 and GNU GPL
Categories:Genome annotation, ab-initio gene prediction, trainable gene prediction
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
mass

MASS is a command-line program written in C to perform fixed-effects (FE) and random-effects (RE) meta-analysis of sequencing studies by combining the score statistics from multiple studies.

Versions:7.1-2
License:n/a
Categories:Application, Biostatistics
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; 11.1.0
License:http://www.wolfram.com/legal/agreements/wolfram-mathematica.html
Categories:mathematics, symbolic algebra
matlab

Matlab programming environment.

Versions:R2016a; R2013b; R2017a
Categories:Programming, mathematics, simulation
matrix2png

Matrix2png is a simple but powerful program for making visualizations of microarray data and many other data types.

Versions:1.2.2
License:GPLv3
Categories:bioinformatics
matstudio

Materials Studio is a complete modeling and simulation environment designed to predict and understand the relationships of a material’s atomic and molecular structure.

Versions:2017R2
License:non-commercial research, http://accelrys.com/about/legal/user-agreements.html
Categories:chemistry, materials science
mauve

Mauve is a system for constructing multiple genome alignments

Versions:2015-02-13
License:GPLv3
Categories:bioinformatics
maven

Maven is a software project management and comprehension tool

Versions:3.3.9
License:GPLv3
Categories:bioinformatics
mcl

The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.

Versions:14-137
License:GNU GPL v3
Categories:Clustering, Graphs
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
mcr

The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components

Versions:9.0.1
License:/sw/sph/centos7/mcr/src/MCR_license.txt
Categories:Mathmatics, Programming, simulation
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-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
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
Current page: 5
Total pages: 9
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