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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
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
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
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Total pages: 10
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