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jags

JAGS is Just Another Gibbs Sampler. It is a program for analysis of

Versions:4.2.0
License:GNU GPL v2
Categories:Bayesian, MCMC, Markov
java

Oracle Java JRE

Versions:1.7.0_80
License:Oracle Binary Code License (BCL)
Categories:System
jellyfish

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.

Versions:2.2.6
License:GPLv3
Categories:bioinformatics
julia

Julia is a high-level, high-performance dynamic language for technical computing. The main homepage for Julia can be found at julialang.org.

Versions:0.5.2; 0.4.6
License:MIT License
Categories:Programming
kallisto

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

Versions:0.43.0
License:Math, Biostatistics, Application
Categories:
kentutils

Jim Kent command line bioinformatic utilities

Versions:302
License:UNKNOWN
Categories:bioinformatics
kmc

KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.

Versions:3.0.1
License:GPL2
Categories:bioinformatics
knitro

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] Knitro is an optimization software library for finding solutions of both continuous optimization models as well as discrete optimization models with integer or binary variables. Knitro is primarily designed for finding local optimal solutions of large sacle continuous nonlinear problems.

Versions:10.1.0-z
License:https://www.artelys.com/en/optimization-tools/knitro
Categories:Optimization, nonlinear solver
ksnp3

kSNP does SNP discovery and SNP annotation from whole genomes

Versions:3.021
License:GPLv2
Categories:bioinformatics
lahey

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

Versions:8.1b
License:http://www.lahey.com/docs/lfpro73help/f95gslicense.htm
Categories:Compiler, f95/f90, fortran
lammps

LAMMPS is a classical molecular dynamics code that models an ensemble of particles.

Versions:31Mar17; 16Feb16; old-15May15
License:http://lammps.sandia.gov/doc/Section_intro.html#open-source-distribution
Categories:molecular dynamics
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
liggghts

LIGGGHTS stands for LAMMPS improved for general granular and granular heat transfer simulations.

Versions:3.7.0
License:https://github.com/CFDEMproject/LIGGGHTS-PUBLIC/blob/master/LICENSE
Categories:molecular dynamics
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
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