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cuda

CUDA compilers and libraries.

Versions:9.1; 6.5; 7.5; 8.0.44; 9.0; 8.0.27rc
License:http://docs.nvidia.com/cuda/eula/index.html
Categories:CUDA, Programming, gpu, library
cudnn

cuDNN libraries.

Versions:7.0-v4; 7.5-v5; 8.0-v5.1; 9.1-v7.1; 8.0-v6.0; 9.0-v7.0; 7.5-v5.1; 6.5-v2
License:http://docs.nvidia.com/cuda/eula
Categories:CUDA, Programming, cuDNN, deep learning, gpu, library, neural network
cufflinks

Transcriptome assembly and differential expression analysis for RNA-Seq.

Versions:2.2.1; 2.2.0; 2.1.1
License:Cufflinks is provided under the OSI-approved Boost License
Categories:bioinformatics
cupti

CUDA Profiler Tools Interface

Versions:8.0.44
License:http://docs.nvidia.com/cuda/eula
Categories:CUDA, Programming, gpu, library, profiler
cutadapt

cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.

Versions:1.14; 1.10
License:Public Domain
Categories:Sequencing, bioinformatics
cyana

CYANA is a program for automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR.

Versions:2.1
License:Commercial
Categories:biophysics NMR
cython

The Cython compiler for writing C extensions for the Python language

Versions:0.16
License:GPLv3
Categories:bioinformatics
dalton

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

Versions:2016
License:http://daltonprogram.org/download/
Categories:ab initio quantum chemistry, electronic structure, materials modeling
delly

Delly2 is an integrated structural variant prediction method

Versions:1.0
License:GNU GPL
Categories:bioinformatics
dendropy

Dendropy is a Python library for phylogenetic computing.

Versions:3.12.0
License:Copyright 2009-2016, Jeet Sukumaran and Mark T. Holder. All rights reserved.
Categories:bioinformatics
diamond

DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.

Versions:0.8.34
License:Open source, citation requested
Categories:bioinformatics sequence align protein blast
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
dsk

DSK: disk streaming K-mers.

Versions:2.1.0
License:???
Categories:Genomics
eems

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

Versions:20161205
License:N/A
Categories:bioinformatics
egglib-cpp

egglib-cpp a C++ library for evolutionary genetics and genomics

Versions:2.1.11
License:indeterminate
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
ENMTools

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).

Versions:1
License:OSL-2.1
Categories:DNA sequence, DNA sequence masking., DNA sequence scanning
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:6.1-171215; 6.2.1; 6.1; 6.2.1-new; 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
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
fastme

A comprehensive, accurate and fast distance-based phylogeny inference program

Versions:2.1.5.1
License:GPL v3
Categories:bioinformatics, phlogenetics
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
fds

Fire Dynamics Simulator (FDS) is a computational fluid dynamics (CFD) model of fire-driven fluid flow. The software solves numerically a form of the Navier-Stokes equations appropriate for low-speed, thermally-driven flow, with an emphasis on smoke and heat transport from fires.

Versions:6.6.0
License:https://www.nist.gov/services-resources/software/fds-and-smokeview
Categories:CFD
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
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Total pages: 11
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