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3D structure prediction software tools | Hi-C data analysis

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3D-GNOME
Web

3D-GNOME 3D GeNOme Modeling Engine

Allows a user without any programing experience to generate 3D structures from…

Allows a user without any programing experience to generate 3D structures from 3C data with minimal effort, and simply requires any modern web browser to access and use. 3D-GNOME provides a…

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ShRec3D
Desktop

ShRec3D

A two-step algorithm and assess its accuracy using both in silico data and…

A two-step algorithm and assess its accuracy using both in silico data and human genome-wide 3C (Hi-C) data. This algorithm avoids convergence issues, accommodates sparse and noisy contact maps, and…

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HSA
Desktop

HSA

Allows to reconstruct 3D chromatin structures at the genome scale by leveraging…

Allows to reconstruct 3D chromatin structures at the genome scale by leveraging multi-track Hi-C data and to model the local dependence of neighboring loci. HSA takes one or more Hi-C contact maps of…

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Chrom3D
Desktop

Chrom3D

Simulates positions of topologically-associated domains (TADs) relative to each…

Simulates positions of topologically-associated domains (TADs) relative to each other and to the nuclear periphery. Chrom3D integrates chromosome conformation capture and lamin-associated domain…

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Chromosome3D
Web
Desktop

Chromosome3D

Reconstructs chromosome three-dimensional models using distance restraints…

Reconstructs chromosome three-dimensional models using distance restraints obtained from Hi-C interaction frequency (IF) data. Chromosome3D is robust with respect to the change of the granularity of…

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LorDG
Desktop

LorDG Lorentzian 3D Genome

A restraint-based method that is capable of reconstructing 3D genome structures…

A restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data. LorDG method is robust to noise and performed well in…

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MOGEN
Desktop

MOGEN

A 3D chromosome reconstruction method to make it capable of reconstructing 3D…

A 3D chromosome reconstruction method to make it capable of reconstructing 3D models of genomes from both intra- and inter-chromosomal Hi-C contact data. We validated MOGEN on synthetic datasets of a…

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FisHiCal
Desktop

FisHiCal

Integrates Hi-C and FISH data, offering a modular and easy-to-use tool for…

Integrates Hi-C and FISH data, offering a modular and easy-to-use tool for chromosomal spatial analysis.

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Gen3D
Desktop

Gen3D

A unique computational approach based on optimization procedures known as…

A unique computational approach based on optimization procedures known as adaptation, simulated annealing, and genetic algorithm to construct 3D models of human chromosomes, using chromosomal contact…

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ISDHiC
Desktop

ISDHiC Inferential Structure Determination Hi-C data

A Bayesian probabilistic framework to view biomolecular structure from…

A Bayesian probabilistic framework to view biomolecular structure from single-cell Hi-C data. ISDHiC computes diverse ensembles of coarse-grained chromosome conformations that reflect the sparsity of…

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miniMDS
Desktop

miniMDS

Infers detailed whole-genome 3D structures by progressively solving and…

Infers detailed whole-genome 3D structures by progressively solving and integrating structures at three resolution levels. miniMDS is a method for inferring structures from Hi-C experiments that is…

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TADbit
Desktop

TADbit

Allows analysis and 3D modelling of 3C-based data. TADbit is a computational…

Allows analysis and 3D modelling of 3C-based data. TADbit is a computational framework including: (i) read quality control and design of the mapping strategy; (ii) mapping of reads to the reference…

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AutoChrom3D
Desktop
Web

AutoChrom3D

An approach for chromatin structure prediction capable of relaxing both kinds…

An approach for chromatin structure prediction capable of relaxing both kinds of sequencing biases by using this identified parameter. This method is validated by intra and inter cell-line…

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PASTIS
Desktop

PASTIS Poisson-based Algorithm for STable Inference of DNA Structure

An approach to infer a consensus 3D structure of a genome from Hi-C data. The…

An approach to infer a consensus 3D 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…

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3D Genome…
Web

3D Genome Browser

Allows users to visualize and explore chromatin interaction data, such as Hi-C,…

Allows users to visualize and explore chromatin interaction data, such as Hi-C, ChIA-PET, Capture Hi-C, PLAC-Seq, and more. 3D Genome Browser also allows users to browse other omics data such as…

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BACH
Desktop

BACH Bayesian 3D constructor for Hi-C data

A Bayesian probabilistic approach to infer the consensus 3D chromosomal…

A Bayesian probabilistic approach to infer the consensus 3D chromosomal structure. In the BACH algorithm, we assume that there exists a consensus 3D chromosomal structure in a cell population. BACH…

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BACH-MIX
Desktop

BACH-MIX

Reveals structural variations of chromatin in a cell population. In the…

Reveals structural variations of chromatin in a cell population. In the BACH-MIX algorithm, we assume that the genomic region of interest is composed of two adjacent sub-regions, each with a rigid…

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MCMC5C
Desktop

MCMC5C

A probabilistic model linking 5C/Hi-C data to physical distances and describe a…

A probabilistic model linking 5C/Hi-C data to physical distances and describe a Markov chain Monte Carlo (MCMC) approach to generate a representative sample from the posterior distribution over…

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ChromSDE
Desktop

ChromSDE

A deterministic method which applies semi-definite programming techniques to…

A deterministic method which applies semi-definite programming techniques to find the best structure fitting the observed data and uses golden section search to find the correct parameter for…

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TADkit
Web
Desktop

TADkit

Produces interactive 3D representations of modelled chromatin conformations.…

Produces interactive 3D representations of modelled chromatin conformations. TADkit allows users to study the relationship between 3D structure of the genome and its biological function. This tool is…

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