Search by title:
Software Item Details
disco

This software is Open Source. Disco is a multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler

Versions:1.1
License:https://github.com/abiswas-odu/Disco
Categories:Genomics
dmtcp

DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications.

Versions:3.0.0
License:https://github.com/dmtcp/dmtcp/blob/master/COPYING
Categories:Programming, Utilities
eems

EEMS uses the concept of effective migration to model the relationship between

Versions:20161205
License:N/A
Categories:bioinformatics
EIG

The EIGENSOFT package implements methods from the following 2 papers:Patterson et al. 2006 PLoS Genet 2:e190 (population structure) Price et al. 2006 Nat Genet 38:904-9 (EIGENSTRAT stratification correction)

Versions:7.2.1
License:GNU GENERAL PUBLIC LICENSE
Categories:bioinformatics
elsa

ELSA: Extended Local Similarity Analysis

Versions:1.0.2
License:GPLv3
Categories:bioinformatics
EMBOSS

EMBOSS is The European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.

Versions:6.6.0
License:GNU GENERAL PUBLIC LICENSE
Categories:bioinformatics
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

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] 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:6.1; 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
espresso-test

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

Versions:6.1
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
examl

Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI. This code implements the popular RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.

Versions:3.0.19
License:GPL3
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
express

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.

Versions:1.5.1
License:GPLv2
Categories:bioinformatics
extrae

Instrumentation framework to generate execution traces of the most used parallel runtimes.

Versions:3.5.1
License:LGPLv2.1
Categories:Instrumentation, Tracing, performance
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
fastool

Simple and quick FastQ and FastA tool for file reading and conversion

Versions:0.1.4-20140711
License:BSD
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; 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
Current page: 3
Total pages: 10
Previous
Next