ChromoPainter

ChromoPainter is a software tool to discover haplotypes in sequenced data. ChromoPainter colors ('paint') each individual as a hybrid of all other sequences. The "coancestry matrix" exposes ancestral associations among individuals. The ChromoPainter algorithm uses the Hidden Markov Model (HMM) and outputs a range of features, such as an expected number of recombination events and sample haplotypes. See fineSTRUCTURE tool and a pipeline for running ChromoPainter for the computation of summaries for admixture events. It can manage thousands of individuals.

Topic

Population genetics;Sequence analysis

Detail

  • Operation: Structure visualisation

  • Software interface: Command-line user interface;Graphical user interface

  • Language: C++

  • License: Attribution-NonCommercial-NoDerivs 3.0 Creative Commons Licence (CC-BY-NC-ND-3.0)

  • Cost: Free

  • Version name: -

  • Credit: Wellcome Trust, Science Foundation of Ireland, the Max Planck Society, Polygene grant.

  • Input: -

  • Output: -

  • Contact: finestructure-discuss@jiscmail.ac.uk, Dan Lawson dan.lawson@bristol.ac.uk

  • Collection: -

  • Maturity: Mature

Publications

  • Inference of population structure using dense haplotype data.
  • Lawson DJ, Hellenthal G, Myers S, Falush D. Inference of population structure using dense haplotype data. PLoS Genet. 2012 Jan;8(1):e1002453. doi: 10.1371/journal.pgen.1002453. Epub 2012 Jan 26. PMID: 22291602; PMCID: PMC3266881.
  • https://doi.org/10.1371/journal.pgen.1002453
  • PMID: 22291602
  • PMC: PMC3266881

Download and documentation

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