bammds

bammds is a tool for visualizing second-generation sequencing samples compared to a reference panel of genotypes using multidimensional scaling, with a focus on determining the ancestry of ancient DNA samples with low amounts of data. The software is available under GNU General Public License v3 and uses R, parallel, and samtools. Test datasets are available on the website, and the tool can be accessed through the email bammds-users@nongnu.org.

Topic

Genetics;Population genetics;Statistics and probability

Detail

  • Operation: Visualisation

  • Software interface: Command-line user interface

  • Language: -

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: Swiss NSF, the ‘Consejo Nacional de Ciencia y Tecnología’ (Mexico), the US NSF, the Lundbeck Foundation and the Danish National Research Foundation.

  • Input: -

  • Output: -

  • Contact: bammds-users@nongnu.org

  • Collection: -

  • Maturity: -

Publications

  • bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).
  • Malaspinas AS, et al. bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS). bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS). 2014; 30:2962-4. doi: 10.1093/bioinformatics/btu410
  • https://doi.org/10.1093/bioinformatics/btu410
  • PMID: 24974206
  • PMC: PMC4184259

Download and documentation

    Currently not available or not maintained.

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