{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T00:33:45Z","timestamp":1767918825921,"version":"3.49.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: All current mitochondrial haplogroup classification tools require variants to be detected from an alignment with the reference sequence and to be properly named according to the canonical nomenclature standards for describing mitochondrial variants, before they can be compared with the haplogroup determining polymorphisms. With the emergence of high-throughput sequencing technologies and hence greater availability of mitochondrial genome sequences, there is a strong need for an automated haplogroup classification tool that is alignment-free and agnostic to reference sequence.<\/jats:p>\n               <jats:p>Results: We have developed a novel mitochondrial genome haplogroup-defining algorithm using a k-mer approach namely Phy-Mer. Phy-Mer performs equally well as the leading haplogroup classifier, HaploGrep, while avoiding the errors that may occur when preparing variants to required formats and notations. We have further expanded Phy-Mer functionality such that next-generation sequencing data can be used directly as input.<\/jats:p>\n               <jats:p>Availability and implementation: Phy-Mer is publicly available under the GNU Affero General Public License v3.0 on GitHub (https:\/\/github.com\/danielnavarrogomez\/phy-mer).<\/jats:p>\n               <jats:p>Contact: \u00a0Xiaowu_Gai@meei.harvard.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu825","type":"journal-article","created":{"date-parts":[[2014,12,14]],"date-time":"2014-12-14T01:33:54Z","timestamp":1418520834000},"page":"1310-1312","source":"Crossref","is-referenced-by-count":62,"title":["Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier"],"prefix":"10.1093","volume":"31","author":[{"given":"Daniel","family":"Navarro-Gomez","sequence":"first","affiliation":[{"name":"1 Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, 2Center for Biomedical Informaticsand 3Center for Mitochondrial and Epigenomic Medicine, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA, 4Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, 5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, 6Division of Human Genetics, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA and 7Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands"}]},{"given":"Jeremy","family":"Leipzig","sequence":"additional","affiliation":[{"name":"1 Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, 2Center for Biomedical Informaticsand 3Center for Mitochondrial and Epigenomic Medicine, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA, 4Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, 5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, 6Division of Human Genetics, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA and 7Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands"}]},{"given":"Lishuang","family":"Shen","sequence":"additional","affiliation":[{"name":"1 Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, 2Center for Biomedical Informaticsand 3Center for Mitochondrial and Epigenomic Medicine, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA, 4Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, 5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, 6Division of Human Genetics, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA and 7Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands"}]},{"given":"Marie","family":"Lott","sequence":"additional","affiliation":[{"name":"1 Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, 2Center for Biomedical Informaticsand 3Center for Mitochondrial and Epigenomic Medicine, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA, 4Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, 5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, 6Division of Human Genetics, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA and 7Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands"}]},{"given":"Alphons P.M.","family":"Stassen","sequence":"additional","affiliation":[{"name":"1 Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, 2Center for Biomedical Informaticsand 3Center for Mitochondrial and Epigenomic Medicine, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA, 4Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, 5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, 6Division of Human Genetics, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA and 7Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands"}]},{"given":"Douglas C.","family":"Wallace","sequence":"additional","affiliation":[{"name":"1 Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, 2Center for Biomedical Informaticsand 3Center for Mitochondrial and Epigenomic Medicine, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA, 4Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, 5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, 6Division of Human Genetics, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA and 7Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands"},{"name":"1 Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, 2Center for Biomedical Informaticsand 3Center for Mitochondrial and Epigenomic Medicine, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA, 4Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, 5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, 6Division of Human Genetics, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA and 7Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands"}]},{"given":"Janey L.","family":"Wiggs","sequence":"additional","affiliation":[{"name":"1 Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, 2Center for Biomedical Informaticsand 3Center for Mitochondrial and Epigenomic Medicine, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA, 4Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, 5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, 6Division of Human Genetics, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA and 7Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands"}]},{"given":"Marni J.","family":"Falk","sequence":"additional","affiliation":[{"name":"1 Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, 2Center for Biomedical Informaticsand 3Center for Mitochondrial and Epigenomic Medicine, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA, 4Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, 5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, 6Division of Human Genetics, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA and 7Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands"},{"name":"1 Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, 2Center for Biomedical Informaticsand 3Center for Mitochondrial and Epigenomic Medicine, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA, 4Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, 5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, 6Division of Human Genetics, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA and 7Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands"}]},{"given":"Mannis","family":"van Oven","sequence":"additional","affiliation":[{"name":"1 Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, 2Center for Biomedical Informaticsand 3Center for Mitochondrial and Epigenomic Medicine, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA, 4Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, 5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, 6Division of Human Genetics, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA and 7Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands"}]},{"given":"Xiaowu","family":"Gai","sequence":"additional","affiliation":[{"name":"1 Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA, 2Center for Biomedical Informaticsand 3Center for Mitochondrial and Epigenomic Medicine, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA, 4Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands, 5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA, 6Division of Human Genetics, The Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA and 7Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2014,12,12]]},"reference":[{"key":"2023051309021123200_btu825-B1","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/290457a0","article-title":"Sequence and organization of the human mitochondrial genome","volume":"290","author":"Anderson","year":"1981","journal-title":"Nature"},{"key":"2023051309021123200_btu825-B2","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1038\/13779","article-title":"Reanalysis and revision of the Cambridge reference 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