{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T17:50:35Z","timestamp":1776361835080,"version":"3.51.2"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,11,7]],"date-time":"2016-11-07T00:00:00Z","timestamp":1478476800000},"content-version":"vor","delay-in-days":863,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 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\u2014typical of ancient DNA data\u2014particularly when only low amounts of data are available for those samples.<\/jats:p>\n               <jats:p>Availability and implementation: 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 ).<\/jats:p>\n               <jats:p>Contact: \u00a0bammds-users@nongnu.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu410","type":"journal-article","created":{"date-parts":[[2014,6,29]],"date-time":"2014-06-29T00:12:32Z","timestamp":1404000752000},"page":"2962-2964","source":"Crossref","is-referenced-by-count":44,"title":["<i>bammds:<\/i>\n             a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)"],"prefix":"10.1093","volume":"30","author":[{"given":"Anna-Sapfo","family":"Malaspinas","sequence":"first","affiliation":[{"name":"1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, 2 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, 3 Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, 4 Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, 5 Ancestry.com DNA LLC, San Francisco, CA 94107, 6 Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, 7 INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarr\u00eda, Argentina and 8 Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ole","family":"Tange","sequence":"additional","affiliation":[{"name":"1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, 2 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, 3 Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, 4 Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, 5 Ancestry.com DNA LLC, San Francisco, CA 94107, 6 Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, 7 INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarr\u00eda, Argentina and 8 Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jos\u00e9 V\u00edctor","family":"Moreno-Mayar","sequence":"additional","affiliation":[{"name":"1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, 2 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, 3 Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, 4 Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, 5 Ancestry.com DNA LLC, San Francisco, CA 94107, 6 Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, 7 INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarr\u00eda, Argentina and 8 Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Morten","family":"Rasmussen","sequence":"additional","affiliation":[{"name":"1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, 2 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, 3 Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, 4 Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, 5 Ancestry.com DNA LLC, San Francisco, CA 94107, 6 Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, 7 INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarr\u00eda, Argentina and 8 Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina"},{"name":"1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, 2 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, 3 Department of Biology, Pennsylvania State 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University, Wartik Laboratory, University Park, PA 16802, 4 Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, 5 Ancestry.com DNA LLC, San Francisco, CA 94107, 6 Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, 7 INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarr\u00eda, Argentina and 8 Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yong","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, 2 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, 3 Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, 4 Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, 5 Ancestry.com DNA LLC, San Francisco, CA 94107, 6 Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, 7 INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarr\u00eda, Argentina and 8 Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina"},{"name":"1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, 2 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, 3 Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, 4 Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and 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Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, 7 INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarr\u00eda, Argentina and 8 Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina"},{"name":"1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, 2 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, 3 Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, 4 Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, 5 Ancestry.com DNA LLC, San Francisco, CA 94107, 6 Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, 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