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gsl

GNU scientific libraries

Versions:2.1; 1.16
License:GPL
Categories:Programming, library, mathematics
gtsuite

GT-SUITE is a versatile multi-physics platform for constructing models of general systems.

Versions:2017
License:Non-commercial research, Academic Institution License Agreement
Categories:CFD, acoustics, chemistry, dynamics, mechanical, multi-physics, thermal
gubbins

Genealogies Unbiased By recomBinations In Nucleotide Sequences

Versions:1.3.4
License:GPLv2
Categories:bioinformatics
gurobi

Gurobi optimization problem solver.

Versions:6.5.2
License:http://www.gurobi.com/pdfs/eula/eula-gurobi.pdf
Categories:Optimization, linear programming
hadoop

Configure Java for Hadoop

Versions:1.2
License:Not applicable
Categories:Utility
harminv

Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion – given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.

Versions:1.4
License:GPLv3
Categories:FDM, filter diagonalization method, harmonic inversion
hdf5

HDF5 data libraries and utilities.

Versions:1.8.16 with gcc/4.8.5; 1.8.16 with gcc/4.9.3; 1.8.16 with gcc/5.4.0; 1.8.16 with intel/14.0.2; 1.8.16 with intel/16.0.3; 1.8.16 with intel/17.0.1; 1.8.16 with pgi/16.4
License:https://www.hdfgroup.org/products/licenses.html
Categories:Programming, Utility, library
hdf5-par

HDF5 data libraries and utilities.

Versions:1.8.16 with gcc/4.8.5; 1.8.16 with gcc/4.9.3; 1.8.16 with intel/14.0.2; 1.8.16 with intel/16.0.3; 1.8.16 with intel/17.0.1
License:https://www.hdfgroup.org/products/licenses.html
Categories:Programming, Utility, library
helios

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] HELIOS Generalized Geometry Lattice Analysis package. Includes Casmo and Simulate from teh Studsvik suite.

Versions:1.12
License:N/A
Categories:Geometry Lattice Analysis, hexagonal VVER reactors, non-LWR lattices
hello

Hello world example of writing a module.

Versions:1.2
License:GPL
Categories:Utility, example, template
hic-pro

HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps.

Versions:2.7.9
License:GPLv2
Categories:bioinformatics
hisat2

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome).

Versions:2.0.5; 2.0.4
License:http://www.gnu.org/licenses/gpl-3.0.html
Categories:Application, Biostatistics, python
hmmer

HMMER: biosequence analysis using profile hidden Markov models

Versions:3.1b2; 3.0
License:GNU GPL v3
Categories:Markov, Sequencing, bioinformatics
homer

HOMER is a suite of tools for Motif Discovery and ChIP-Seq analysis.

Versions:4.8
License:GPLv3
Categories:bioinformatics
HTSeq

a swiss-army knife of tools for a wide-range of genomics analysis tasks.

Versions:2.20.1
License:GPLv2
Categories:bioinformatics
htslib

C library for high-throughput sequencing data formats

Versions:1.1; 1.3.2
License:GPLv2
Categories:bioinformatics
hyperworks

A suite of CAE software products.

Versions:2017
License:CFD, Structural Analysis, Multi-body
Categories:
hypre

XCrySDen is a molecular/crystal structure visualization program.

Versions:2.11.2
License:http://www.xcrysden.org/License.html
Categories:crystal symmetries, electronic structure, vizualization
idba

A Practical Iterative De Bruijn Graph De Novo Assembler related to Sequence assembly problem in bioinfomatics.

Versions:1.1.3
License:GPL2
Categories:bioinforatics sequencing
idl

IDL analysis and visualization software.

Versions:8.5
License:http://www.harrisgeospatial.com/company/legal/eula.aspx
Categories:Visualization
image-libraries

Image libraries

Versions:160610; 170303
License:more than one
Categories:Programming, gif, jpeg, libraries, png
impi

Intel MPI runtime library.

Versions:5.1.3
License:Not provided
Categories:MPI, library
impute

IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes. Most people use just a couple of the program’s basic functions, but we have also built up a collection of specialized and powerful options. If you are new to IMPUTE2, or indeed to phasing and imputation in general, we suggest that you start by learning the basics.

Versions:2.3.2
License:http://www.gnu.org/licenses/gpl.html
Categories:Application, Biostatistics, Math
indri

Indri is a search engine that provides state-of-the-art text search and a rich structured query language for text collections

Versions:5.9
License:GPLv2
Categories:bioinformatics
intel

Intel compiler suite.

Versions:14.0.2; 16.0.3; 17.0.1
License:None provided
Categories:Core, Development, library
intel-tbb

Intel Threading Building Blocks (Intel TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable and composable, and that have future-proof scalability.

Versions:4.4-u5
License:GNU GPL v2
Categories:Programming, TBB, libraries
ipminer

a swiss-army knife of tools for a wide-range of genomics analysis tasks.

Versions:1.0
License:GPLv2
Categories:bioinformatics
ipopt

Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale ?nonlinear optimization.

Versions:3.12.6
License:https://projects.coin-or.org/Ipopt
Categories:nonlinear optimization
ipyrad

ipyrad is a toolbox for assembly and analysis of RAD-seq type genomic data sets

Versions:0.4.4; 0.5.15; 0.6.17; 0.4.1; 0.6.8
License:GPL3
Categories:bioinforatics assembly rad
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:16Feb16; old-15May15
License:http://lammps.sandia.gov/doc/Section_intro.html#open-source-distribution
Categories:molecular dynamics
Current page: 4
Total pages: 9
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