Software for analyzing 3C-based data The 3DG site at the Dekker Lab (UMASS, Worcester, USA).

To facilitate 5C experiment workflow, the Dekker lab has a full suite of web-based tools for the design, analysis and data visualization of chromatin interaction experiments. These tools allow users to design a 5C experiment for any given locus / species and ease them through the primer layout and filtering processes. Once designed a full spectrum of analysis, integration and visualizations tools become available.
The HiCLib at the Mirny Lab (MIT, Boston, USA).

The HiCLib is a collection of tools to map, filter and analyze Hi-C data. The library is written in Python, an easy-to-learn human-friendly programming language.
The HiC-Pro at the Barillot Lab (IC, Paris, France).

HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps.
The HiFive at the Taylor and Corces Labs (Emory, Atlanta, USA).

HiFive is a Python package for normalization and analysis of chromatin structural data produced using either the 5C of HiC assay. This library contains tools for handling all steps after mapping of reads.
The HSA at the Ouyang Lab (JAX, Connecticut, USA).

HSA is is a flexible tool that can jointly analyze multiple contact maps from Hi-C experiments to infer the 3D chromatin structure of the genome.
The Juicebox at the Lieberman-Aiden Lab (Center for Genome Architecture, Houston, USA).

Juicebox is our software for visualizing data from proximity ligation experiments, such as Hi-C, 5C, and Chia-PET. It allows you to visually navigate the 3D proximity map dataset and explore entire human genomes.
The TADbit software at the Marti-Renom Lab (CNAG-CRG, Barcelona, Spain).

TADbit is an easy-to-use Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models.
Software for modeling 3C-based data The AutoChrom3D software at the Zhang Lab (Huazhong Agricultural University, China).

AutoChrom3D uses datasets from 3C, 4C and 5C experiments to predict their chromatin structures.
The BACH software at the Liu Lab (Harvard, Boston, USA).

BACH is a novel Bayesian probabilistic approach for analyzing Hi-C data. BACH takes the Hi-C contact matrix and local genomic features (restriction enzyme cutting frequencies, GC content and sequence uniqueness) as input and produces, via MCMC computation, the posterior distribution of three-dimensional (3D) chromosomal structure.
The ChromSDE software at the Sung Lab (NUS, Singapore).

ChromSDE inferences the spatial organization of chromosomes using a semi-definte embedding approach and Hi-C data
The Gen3D at the Cheng Lab (UM, Columbia, USA).

Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations. This method can generate three-dimensional chromosomal models satisfying a large portion of chromosomal contacts.
The HiFive at the Taylor and Corces Labs (Emory, Atlanta, USA).

HiFive is a Python package for normalization and analysis of chromatin structural data produced using either the 5C of HiC assay. This library contains tools for handling all steps after mapping of reads.
The HSA at the Ouyang Lab (JAX, Connecticut, USA).

HSA is is a flexible tool that can jointly analyze multiple contact maps from Hi-C experiments to infer the 3D chromatin structure of the genome.
The The MCMC5C software at the Dostie and Blanchett Labs (McGull, Montreal, Canada).

MCMC5C uses a MonteCarlo approach for identifying the likely 3D structure of a genomic domain informed by 5C data.
The PASTIS software at the Vert Lab (MINES-IC, Paris, France).

PASTIS proposes a novel approach to infer a consensus three- dimensional structure of a genome from Hi-C data. The method incorporates a statistical model of the contact counts, assuming that the counts between two loci follow a Poisson distribution whose intensity decreases with the physical distances between the loci. The method can automatically adjust the transfer function relating the spatial distance to the Poisson intensity and infer a genome structure that best explains the observed data.
The Shrec3D software at the Mozziconacci Lab (PMCU, Paris, France).

Shrec3D is a program that aims at reconstructing a genome 3D structure (b) from the sole knowledge of the contacts between different genomic regions (a) as determined by Hi-C.
The TADbit software at the Marti-Renom Lab (CNAG-CRG, Barcelona, Spain).

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify adn compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models.
Software for visualizing 3D models The Genome3D software at the Tang (USC, South Carolina, USA) and Zheng Labs (UTH, Texas, USA).

The Genome3D is a model-view framework for displaying genomic and epigenomic data within a three-dimensional physical model of the human genome. In this framework, the model of the physical genome implicitly contains all levels of structure and hierarchy, and provides an underlying platform for integrating multi-scale structural and genomic information within three dimensions.
The GMol at the Cheng Lab (UM, Columbia, USA).

GMol is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group.
The TADkit software at the Marti-Renom Lab (CNAG-CRG, Barcelona, Spain).

TADkit is a JavaScript based visualizer for 3D genomic data that helps researchers to easy annotate 3D models generated by TADbit. TADkit is open-source with a interactive visual interface built from the standard JavaScript libraries such as AngularJS, ThreeJS and D3.