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Volume 22
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10.3390/ijms22115747
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Article

Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences

by
Arne Dür
1,
Nicole Huber
2 and
Walther Parson
2,3,*
1
Institute of Mathematics, University of Innsbruck, 6020 Innsbruck, Austria
2
Institute of Legal Medicine, Innsbruck Medical University, 6020 Innsbruck, Austria
3
Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2021, 22(11), 5747; https://doi.org/10.3390/ijms22115747
Submission received: 6 May 2021 / Revised: 25 May 2021 / Accepted: 26 May 2021 / Published: 27 May 2021
(This article belongs to the Special Issue Mitochondrial DNA and RNA)
Review Reports Versions Notes

Abstract

In this paper, we present a new algorithm for alignment and haplogroup estimation of mitochondrial DNA (mtDNA) sequences. Based on 26,011 vetted full mitogenome sequences, we refined the 5435 original haplogroup motifs of Phylotree Build 17 without changing the haplogroup nomenclature. We adapted 430 motifs (about 8%) and added 966 motifs for yet undetermined subclades. In summary, this led to an 18% increase of haplogroup defining motifs for full mitogenomes and a 30% increase for the mtDNA control region that is of interest for a variety of scientific disciplines, such as medical, population and forensic genetics. The new algorithm is implemented in the EMPOP mtDNA database and is freely accessible.
Keywords: mitochondrial DNA; phylogeny; haplogroup; alignment mitochondrial DNA; phylogeny; haplogroup; alignment

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MDPI and ACS Style

Dür, A.; Huber, N.; Parson, W. Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences. Int. J. Mol. Sci. 2021, 22, 5747. https://doi.org/10.3390/ijms22115747

AMA Style

Dür A, Huber N, Parson W. Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences. International Journal of Molecular Sciences. 2021; 22(11):5747. https://doi.org/10.3390/ijms22115747

Chicago/Turabian Style

Dür, Arne, Nicole Huber, and Walther Parson. 2021. "Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences" International Journal of Molecular Sciences 22, no. 11: 5747. https://doi.org/10.3390/ijms22115747

APA Style

Dür, A., Huber, N., & Parson, W. (2021). Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences. International Journal of Molecular Sciences, 22(11), 5747. https://doi.org/10.3390/ijms22115747

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