title: bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).
abstract: CONCLUSIONS
  We present bammds, a practical tool that allows visualization of samples sequenced by second-generation sequencing when compared with a reference panel of individuals (usually genotypes) using a multidimensional scaling algorithm. Our tool is aimed at determining the ancestry of unknown samples-typical of ancient DNA data-particularly when only low amounts of data are available for those samples.
  
  
  METHODS
  The software package is available under GNU General Public License v3 and is freely available together with test datasets https://savannah.nongnu.org/projects/bammds/. It is using R (http://www.r-project.org/), parallel (http://www.gnu.org/software/parallel/), samtools (https://github.com/samtools/samtools).
  
  
  BACKGROUND
  bammds-users@nongnu.org
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina.
authors: Anna-Sapfo
authors: AS
authors: Malaspinas
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina.
authors: Ole
authors: O
authors: Tange
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina.
authors: José Víctor
authors: JV
authors: Moreno-Mayar
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina.
authors: Morten
authors: M
authors: Rasmussen
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina.
authors: Michael
authors: M
authors: DeGiorgio
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina.
authors: Yong
authors: Y
authors: Wang
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina.
authors: Cristina E
authors: CE
authors: Valdiosera
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina.
authors: Gustavo
authors: G
authors: Politis
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina.
authors: Eske
authors: E
authors: Willerslev
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina.
authors: Rasmus
authors: R
authors: Nielsen
mesh_terms: D005828:Genetics, Population; D015894:Genome, Human / Q000235:genetics; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006801:Humans; D058974:Phylogeography / Q000379:methods*; D012984:Software