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bowtie2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Versions:2.1.0; 2.3.2; 2.3.1; 2.2.9
License:GPLv3
Categories:bioinformatics
bsclient

bsclient is a simple FTP-like command-line client for accessing and downloading data from an Illumina BASESPACE account.

Versions:0.4.1a
License:GPLv3
Categories:bioinformatics
bucky

BUCKy is a free program to combine molecular data from multiple loci.

Versions:1.4.4
License:GPL v2
Categories:BCA, Bayesian, Concordance
bwa

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.

Versions:0.7.3a; 0.5.9; 0.7.8; 0.7.15
License:GPLv3
Categories:bioinformatics
caffe

Caffe is a deep learning framework made with expression, speed, and modularity in mind.

Versions:170407; 160803
License:https://github.com/BVLC/caffe/blob/master/LICENSE
Categories:deep learning, machine learning
canu

A single molecule sequence assembler for genomes large and small.

Versions:1.3
Categories:Sequencing, bioinformatics
cap3

CAP3 is the third generation of the CAP sequence assembly program.

Versions:2015-02-10
License:GPLv3
Categories:bioinformatics
cd-hit

CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses.

Versions:4.6.4; 2016-0711
Categories:
cegma

CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome.

Versions:2.5
License:GNU GPL v2
Categories:bioinformatics
cellprofiler

CellProfiler is free, open-source software for quantitative analysis of biological images.

Versions:3.0.0rc1-20170814
License:BSD 3-clause license
Categories:analysis, bioinformatics, biology, imaging
centrifuge

Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems.

Versions:1.0.3-beta; 1.0.2-beta
License:GPL3
Categories:bioinformatices sequencing indexing gene classifications reads genome
cfitsio

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

Versions:3.390
License:Public Domain
Categories:Astronomy, FITS, Image
chemkin

Chemkin is for modeling and simulating complex gas phase and surface chemistry reactions that are used for the conceptual development of combustion systems.

Versions:17.1; 18.1
Categories:combustion
circos

Circos description

Versions:0.69-3
License:GPLv3
Categories:bioinformatics
clang

The goal of the Clang project is to create a new C, C++, Objective C and Objective C++ front-end for the LLVM compiler.

Versions:3.8.1
License:University of Illinois/NCSA Open Source License
Categories:Compiler, LLVM
clonalframeml

A software package that performs efficient inference of recombination in bacterial genomes. ClonalFrameML can be applied to any type of aligned sequence data, but is especially aimed at analysis of whole genome sequences.

Versions:1.0-19
License:GNU GPL v3 https://www.gnu.org/copyleft/gpl.html
Categories:Biostatistics, Software
close_kmers

Generate AMR classifiers using a bespoke implementation that is designed for finding the k-mers that are indicative of resistance

Versions:20160810
License:public domain, see http://www.theseed.org/wiki/DownloadPage
Categories:bioinformatics
cmake

CMake cross-platform make system.

Versions:3.5.2
License:https://cmake.org/licensing/
Categories:Compiler, Programming, Utility
cobrapy

Constraints-based modeling of biological networks.

Versions:0.5.11
License:LGPL, GPL
Categories:biology, cobra, gurobi, modeling, networks, python
comsol

COMSOL is multiphysics simulation software. Note, COMSOL is no longer supported and is available ‘as is’. We do not have an active support agreement with COMSOL, and we cannot obtain newer releases. COMSOL is only available from the Flux on-campus cluster.

Versions:5.1; 5.3
License:Not available
Categories:multiphysics, simulation
concoct

A program for unsupervised binning of metagenomic contigs

Versions:0.4.0; 0.4.1
License:GPLv2
Categories:bioinformatics
converge

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] CONVERGE is a CFD code with adaptive meshing.

Versions:2.2.0_082115; 2.3.20_021417; 2.1.0_111615; 2.3.13_180716
License:Provided by licensed labs
Categories:CFD, Fluid dynamics, adaptive mesh
cplex

CPLEX is a high-performance optimizer for linear programming

Versions:12.6.2
License:https://developer.ibm.com/academic/
Categories:linear programming, optimizer
crt

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats.

Versions:1.2
License:GPLv3
Categories:bioinformatics
cubit

CUBIT is a full-featured software toolkit for robust generation of two- and three-dimensional finite element meshes.

Versions:13.2
License:https://cubit.sandia.gov/public/licensing.html
Categories:mesh
cuda

CUDA compilers and libraries.

Versions:6.5; 7.5; 8.0.44; 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; 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:1.10
License:Public Domain
Categories:Sequencing, bioinformatics
cython

The Cython compiler for writing C extensions for the Python language

Versions:0.16
License:GPLv3
Categories:bioinformatics
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
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
Current page: 2
Total pages: 9
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