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blasr

Pacbio utilites for various sequence alignment tasks

Versions:5.1
License:GPLv2
Categories:bioinformatics
blat

Standalone blat sequence search command line tool

Versions:34x1
License:GPLv2
Categories:bioinformatics
blender

Blender is a professional free and open-source 3D computer graphics software product used for creating animated films, visual effects, art, 3D printed models, interactive 3D applications and video games

Versions:2.78c
License:https://www.blender.org/about/license
Categories:3D modeling, simulation, vizualization
bless

Bloom-filter-based Error Correction Solution for High-throughput Sequencing Reads

Versions:1.02
License:GPL v3
Categories:bioinformatics sequencing
boost

Boost C++ library collection.

Versions:1.61.0; 1.64.0; 1.57.0
License:http://www.boost.org/users/license.html
Categories:C++, Programming, library
boost-dev

Boost C++ library collection.

Versions:1.61.0
License:http://www.boost.org/users/license.html
Categories:C++, Programming, library
bowtie

Bowtie is an ultrafast, memory-efficient short read aligner.

Versions:1.0.0
License:GPLv3
Categories:bioinformatics
bowtie2

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

Versions:2.1.0; 2.3.3; 2.3.2; 2.3.1; 2.2.9
License:GPLv3
Categories:bioinformatics
bpp-core

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics.

Versions:2.4.0
License:CeCILL 3
Categories:bioinformatics
bpp-popgen

bpp-popgen: This library provides classes for population genetics analysis.

Versions:2.4.0
License:CeCILL 3
Categories:bioinformatics
bpp-seq

bpp-seq: This library provides classes to store and analyse biological sequences.

Versions:2.4.0
License:CeCILL 3
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
busco

BUSCO v3 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9.

Versions:3.0.2
License:MIT License
Categories:bioinformatics
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
cafe

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

Versions:4.1
License:https://github.com/hahnlab/CAFE/blob/master/LICENSE
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; 2.2.0
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
CLHEP

A Class Library for High Energy Physics

Versions:2.4.0.2
License:GPL
Categories:Research Development
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:3.11.1; 3.5.2
License:https://cmake.org/licensing/
Categories:Compiler, Programming, Utility
coalgf

Compute the probability distribution of gene tree histories and gene tree topolgies for a fixed three-taxon species tree under the coalescent model with gene flow between both pairs of sister population.

Versions:1.0
License:GPLv3
Categories:bioinforatics
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; 5.3a
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; 2.3.27; 2.3.20_021417; 2.1.0_111615; 2.4.14; 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
crystal

crystal evaluates crystaline solids.

Versions:17-demo
License:http://www.crystal.unito.it/license-fee.php
Categories:materials science
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
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Total pages: 11
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