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fftw

Libraries for computation of discrete Fourier transform.

Versions:3.3.4 with gcc/4.8.5; 3.3.4 with gcc/4.9.3; 3.3.4 with gcc/5.4.0; 3.3.4 with intel/14.0.2; 3.3.4 with intel/16.0.3; 3.3.4 with intel/17.0.1; 3.3.6-pl2-lsa with gcc/4.8.5; 2.1.5 with gcc/4.8.5; 2.1.5 with intel/16.0.3
License:http://www.fftw.org/fftw3_doc/License-and-Copyright.html
Categories:Core, Development, library
fiji

Fiji is an image processing package—(a batteries-included) distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

Versions:1.52a
License:GPLv2
Categories:bioinformatics
flex

Lexical analyser generators

Versions:2.6.2
License:more than one
Categories:Programming, bison, flex, lex, libraries, yacc
flexbar

The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences.

Versions:2.7.0
Categories:Sequencing, bioinformatics
flexlm

FLEXlm utility programs.

Versions:11.11.1.2
License:None provided
Categories:Utility
flux-utils

flux-utils is a collection of utilities for the Flux and Armis HPC clusters.

Versions:1.0
License:GPL-3
Categories:Armis, Flux, Utilities
freebayes

Bayesian genetic variant detector designed to find small polymorphisms

Versions:1.0.2.33
License:MIT software license
Categories:bioinformatics genetics bayesian detector polymorphisms
freesurfer

FreeSurfer MRI processing and analysis software.

Versions:6.0.0; 5.3.0
License:http://freesurfer.net/fswiki/FreeSurferSoftwareLicense
Categories:MRI, neuroimaging, neuroscience
fsl

FSL suite of MRI neuroimaging tools.

Versions:5.0.9; 5.0.10
License:http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
Categories:DTI, fMRI, neuroimaging, neuroscience
g95

G95 – f95/f90 fortran compiler

Versions:0.94
License:fortran, compiler
Categories:
GAMESS

The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.

Versions:2018R1
License:Non-standard research-group license: http://www.msg.ameslab.gov/gamess/License_Agreement.html
Categories:ab initio molecular quantum chemistry, wavefunction computation
gatk

The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it’s a suite of tools for working with the human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and local realigner.

Versions:4.0.0; 3.4.0; 3.2-2; 3.5; 3.6
License:Broad Institute Software License Agreement
Categories:bioinformatics
gaussian

Gaussian is an electronic structure program that predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types.

Versions:16-revA03-avx2; 16-revA03-avx; 09-revD01; 16-revA03; 09-revE01
License:Academic, noncommercial research and instructional use only
Categories:electronic structure, molecular
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
glimmer

Microbial Gene-Finding System

Versions:3.02
License:GPLv2
Categories:bioinformatics
GlimmerHMM

Eukaryotic Gene-Finding System

Versions:3.0.4
License:GPLv2
Categories:bioinformatics
globus

Provides an interface to Globus services from the shell, and is suited to both interactive

Versions:1.4.0
License:Apache 2.0
Categories:File Transfer, Utilities
gloome

A C++ shell program for the detection of gain ans loss events

Versions:1.266
License:GPLv3
Categories:bioinformatics
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; 1.10.1
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
gstreamer

GStreamer is a library for constructing graphs of media-handling components.

Versions:1.12.4
License:https://gstreamer.freedesktop.org/documentation/plugin-development/appendix/licensing-advisory.html
Categories:audio, codec, video
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
Current page: 4
Total pages: 11
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