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gcc

GNU compiler suite

Versions:4.8.5; 7.2.0; 4.9.3; 5.4.0
License:GPL
Categories:Compiler, Development, Programming
gdal

GDAL is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation.

Versions:2.1.0
License:MIT (http://svn.osgeo.org/gdal/trunk/gdal/LICENSE.TXT)
Categories:GIS, Geospatial, OGR
geant

is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

Versions:4.10.03.p01
License:http://geant4.web.cern.ch/geant4/license/LICENSE.html
Categories:libraries, physics, simulation
gemini

GEMINI – integrative exploration of genetic variation and genome annotations.

Versions:0.19.1
License:GPLv2
Categories:bioinformatics
geneid

geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure.

Versions:1.4.4
License:GNU GPL v2
Categories:bioinformatics
genometools

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt.

Versions:1.5.9
License:GPLv3
Categories:bioinformatics
geos

GEOS (Geometry Engine – Open Source) is a C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions.

Versions:3.5.0
License:GNU LGPL v2.1
Categories:GIS, Geometry, OSGeo
gepard

Gepard allows the calculation of 5 dotplots even for large sequences like chromosomes or bacterial genomes.

Versions:1.40
License:GPLv3
Categories:bioinformatics
gffcompare

The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the ‘query’ files), when compared with a reference annotation (also provided as GFF).

Versions:0.9.7
License:https://opensource.org/licenses/Artistic-2.0
Categories:Application, Math, bioinformatics
ghostscript

Ghostscript is an interpreter for the PostScript language and for PDF.

Versions:9.19
License:GPLv3
Categories:bioinformatics
git

Git version control software

Versions:2.13.3
License:GPL version 2
Categories:Development, Utility, version control
gmt

an open source collection of tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x–y plots via contour maps to artificially illuminated surfaces and 3D perspective views.

Versions:5.4.2
License:LGPL
Categories:GIS projection map plot geography
go

Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.

Versions:1.7.3; 1.6.2; 1.9; 1.8
License:https://golang.org/LICENSE?m=text
Categories:Go, Programming
gotcloud

GotCloud contains Mapping & Variant Calling Pipelines.

Versions:master
License:GPLv3
Categories:
gpaw

GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).

Versions:1.1.0
License:https://gitlab.com/gpaw/gpaw/blob/master/LICENSE
Categories:ASE, PAW, atomic simulation environment, density-functional theory (DFT), projector-augmented wave
gromacs

GROMACS performs Newtonian simulatons of molecular dynamics.

Versions:4.6.7 with gcc/5.4.0 openmpi/1.10.2; 5.1.2 with gcc/4.9.3 openmpi/1.10.2; 5.1.2 with gcc/5.4.0 openmpi/1.10.2
Categories:
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:7.5.1; 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
imagemagick

ImageMagick® is a software suite to create, edit, compose, or convert bitmap images.

Versions:7.0.7
License:https://www.imagemagick.org/script/license.php
Categories:Programming, libraries, multi-language
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
Current page: 4
Total pages: 10
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