Software package for high-throughput subtomogram classification and averaging. The software can handle hundreds of thousands of subtomograms and therefore allows reference-free mining of protein complexes in whole cell tomograms. The software is currently beta tested in several labs, including the 14 labs of Joachim Frank (Columbia University), Kay Gruenewald (Oxford University) and Martin Beck (EMBL Heidelberg).

Frazier, Z., Xu, M., & Alber, F. (2017). Tomominer and tomominercloud: A software platform for large-scale subtomogram structural analysis. Structure, 25(6), 951-961. Paper

MPP (Multi-Pattern-Pursuit)

“Multi Pattern Pursuit” is a program for proteome-scale discovery of high-quality structural patterns, occurring frequently in a cellular tomogram without using templates of known structures..The program allows template-free detection of macromolecular complexes in cellular tomograms.

Xu, M., Singla, J., Tocheva, E. I., Chang, Y. W., Stevens, R. C., Jensen, G. J., & Alber, F. (2019). De novo structural pattern mining in cellular electron cryotomograms. Structure, 27(4), 679-691. Paper

Hi-C Corrector

Software package for fast and memory-efficient normalization of Hi-C data. HiCorrector is an easy-to-use, open source implementation. Its salient features are (i) scalability; (ii) memory efficiency; (iii) fast speed.

Li, W., Gong, K., Li, Q., Alber, F., & Zhou, X. J. (2015). Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data. Bioinformatics, 31(6), 960-962. Paper


A software package to simultaneously and effieienctly fit all protein component structures into the cryo electron density map of its assembly.

Zhang, S., Vasishtan, D., Xu, M., Topf, M., & Alber, F. (2010). A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps. Bioinformatics, 26(12), i261-i268. Paper

RBM Brownian Dynamics

Software package for particle-based reaction diffusion simulations of complex protein mixtures. The developed algorithm tolerates substantially larger time steps (an order of magnitude) than comparable methods while maintaining high accuracy and obeying the detailed balance rule of equilibrium reactions.

Frazier, Z., & Alber, F. (2012). A Computational Approach to Increase Time Scales in Brownian Dynamics–Based Reaction-Diffusion Modeling. Journal of Computational Biology, 19(6), 606-618. Paper


Topdom is an efficient and deterministic method to identify topological domains in genomes from Hi-C data, along with a set of statistical methods for evaluating their quality. TopDom is much more efficient than existing methods and depends on just one intuitive parameter, for which we provide easy-to implement optimization guidelines.

Shin, H., Shi, Y., Dai, C., Tjong, H., Gong, K., Alber, F., & Zhou, X. J. (2016). TopDom: an efficient and deterministic method for identifying topological domains in genomes. Nucleic acids research, 44(7), e70-e70. Paper

PGS software package

We provide a user-friendly software package that runs on most high-performance computing platforms. Our software package PGS takes a genome-wide Hi-C contact frequency matrix and produces an ensemble of 3D genome structures, entirely consistent with the input Hi-C matrix. The software automatically generates an analysis report, and we also provide tools to extract and analyze the 3D coordinates.

Hua, N., Tjong, H., Shin, H., Gong, K., Zhou, X. J., & Alber, F. (2018). Producing genome structure populations with the dynamic and automated PGS software. Nature protocols, 13(5), 915. Paper