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emirge

EMIRGE reconstructs full length ribosomal genes from short read sequencing data.

Versions:0.60.3
License:GNU GPL v3
Categories:Reconstruction, Sequencing, bioinformatics
ensight101

EnSight is a post processing and visualization tool.

Versions:10.1.6e
License:https://support.ceisoftware.com/hc/en-us/articles/202370327-EnSight-End-User-License-Agreement
Categories:Visualization, processing
espresso

Quantum ESPRESSO is an integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale.

Versions:old-5.1.1; 5.4.0
License:http://www2.mmm.ucar.edu/wrf/users/public.html
Categories:ab initio quantum chemistry, electronic structure, materials modeling
evolver

Surface Evolver is an interactive program for the modelling of liquid surfaces shaped by various forces and constraints

Versions:2.70
License:Free no license
Categories:Geometry, Surfaces
exabayes

ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters.

Versions:1.5
License:GNU GPL v3
Categories:bioinformatics
exonerate

Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.

Versions:2.2.0
License:GPLv3
Categories:Alignment, Sequencing, bioinformatics
fastgear

Software for analysing sequence alignments

Versions:1.0
License:GPLv2
Categories:Biostatistics, Matlab, Software
fastml

Used for the reconstruction of ancestral sequences. gub version adds functionality for gubbins software

Versions:gub; 3.1
License:GPLv2
Categories:bioinformatics
fastqc

A quality control tool for high throughput sequence data.

Versions:0.11.5; 0.10.1
License:GPLv3
Categories:bioinformatics
fastStructure

fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.

Versions:1.0
License:MIT License
Categories:Genotype, bioinformatics
fasttree

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

Versions:2.1.9
License:GPLv3
Categories:bioinformatics
fastx-toolkit

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

Versions:0.0.14
License:GPL3
Categories:bioinformatics reads fasta fastx fastq
fdtd-solutions

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] Lumerical FDTD Solutions is a high performance 3D FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials.

Versions:8.16.903
License:commercial, https://www.lumerical.com/tcad-products/licensing/license_agreement.html
Categories:3D, FDTD, Optimization, analysis, design, maxwell, optics, photonics, solver
ffmpeg

FFMPEG is a complete, cross-platform solution to record, convert and stream audio and video.

Versions:3.0.2; 3.2.4
License:https://ffmpeg.org/legal.html
Categories:audio, codec, transcoder, video
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
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:5.3.0
License:http://freesurfer.net/fswiki/FreeSurferSoftwareLicense
Categories:MRI, neuroimaging, neuroscience
fsl

FSL suite of MRI neuroimaging tools.

Versions:5.0.9
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:
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: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:09-revD01; 09-revE01
Categories:electronic structure, molecular
gcc

GNU compiler suite

Versions:4.8.5; 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
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; 1.8
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:
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