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Papers describing software used in ShoRAH

  1. Zagordi et al. (2011)

    BMC Bioinformatics 2011, 12:119 doi:10.1186/1471-2105-12-119
  2. Bhattacharya A. (2010) Performance optimizations and improved sampling techniques for Dirichlet Process Mixture models
    Bachelor's thesis, BITS Pilani and ETH Zurich
  3. Zagordi et al. (2010)

    J Comput Biol 17(3): 417-428. doi:10.1089/cmb.2009.0164.
  4. Eriksson et al. (2008)

    PLoS Comput Biol 4(5): e1000074. doi:10.1371/journal.pcbi.1000074

Papers using ShoRAH

  1. Astrovskaya et al. (2011)

    accepted (BMC Bioinformatics in proceedings of Recomb-Seq 2011)
  2. Prosperi et al. (2011)

    BMC Bioinformatics (2011) vol. 12 (1) pp. 5
  3. Zagordi et al. (2010)

    Nucleic Acids Research 38: 7400-7409. doi:10.1093/nar/gkq655 See also the available data (link) from the paper.

Other relevant papers

  1. Prabhakaran et al. (2010) HIV-Haplotype Inference using a Constraint-based Dirichlet Process Mixture Model
    Extended abstract presented at NIPS Machine Learning in Computational Biology (MLCB) 2010 workshop


Since version 0.6 of the software, we are hosting the edge version on github The documentation is taking shape here
Short review in Curr. Opin. Virol.
The paper Beerenwinkel, Zagordi (2011) reviews the main challenges in the computational and statistical analysis of viral populations by means of NGS. It also contains a list of the software currently available.


ShoRAH application note published!
If you use our software, please cite Zagordi et al. (2011) BMC Bioinformatics 2011, 12:119 doi:10.1186/1471-2105-12-119