repgenHMM

repgenHMM is a software tool for inferring immune receptor generation rules for early T and B cell development from sequenced data. The repgenHMM uses the Hidden Markov model (HMM) based on the Baum-Welch algorithm.

Topic

Immunology;Sequence analysis;Applied mathematics

Detail

  • Operation: Sequence analysis

  • Software interface: Command-line user interface

  • Language: C++

  • License: Other

  • Cost: Free

  • Version name: -

  • Credit: European Research Council Starting Grant.

  • Input: FASTA, text

  • Output: CSV

  • Contact: Yuval Elhanati elhanati@lpt.ens.fr, Thierry Mora tmora@lps.ens.fr, Aleksandra M. Walczak awalczak@lpt.ens.fr

  • Collection: -

  • Maturity: -

Publications

  • repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data.
  • Elhanati Y, Marcou Q, Mora T, Walczak AM. repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data. Bioinformatics. 2016 Jul 1;32(13):1943-51. doi: 10.1093/bioinformatics/btw112. Epub 2016 Feb 26. PMID: 27153709; PMCID: PMC4920122.
  • https://doi.org/10.1093/bioinformatics/btw112
  • PMID: 27153709
  • PMC: PMC4920122

Download and documentation

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