HaploGrouper: A generalized approach to haplogroup classification

Anuradha Jagadeesan; Sigríður Sunna Ebenesersdóttir; Valdís Björt Guðmundsdóttir; Elisabet Linda Thordardottir; Kristjan Helgi Swerford Moore; Agnar Sturla Helgason

doi:10.1093/bioinformatics/btaa729

HaploGrouper: A generalized approach to haplogroup classification

Anuradha Jagadeesan, Sigríður Sunna Ebenesersdóttir, Valdís Björt Guðmundsdóttir, Elisabet Linda Thordardottir, Kristjan Helgi Swerford Moore, Agnar Sturla Helgason

Faculty of Sociology, Anthropology and Folkloristics

University of Iceland

Research output: Contribution to journal › Article › peer-review

Abstract

MOTIVATION: We introduce HaploGrouper, a versatile software to classify haplotypes into haplogroups on the basis of a known phylogenetic tree. A typical use case for this software is the assignment of haplogroups to human mitochondrial DNA (mtDNA) or Y-chromosome haplotypes. Existing state-of-the-art haplogroup-calling software is typically hard-wired to work only with either mtDNA or Y-chromosome haplotypes from humans.

RESULTS: HaploGrouper exhibits comparable accuracy in these instances and has the advantage of being able to assign haplogroups to any kind of haplotypes from any species-given an extant annotated phylogenetic tree defined by sequence variants.

AVAILABILITY AND IMPLEMENTATION: The software is available at the following URL https://gitlab.com/bio_anth_decode/haploGrouper.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original language	English
Pages (from-to)	570-572
Number of pages	3
Journal	Bioinformatics
Volume	37
Issue number	4
DOIs	https://doi.org/10.1093/bioinformatics/btaa729
Publication status	Published - 1 May 2021

Bibliographical note

Other keywords

Genes
Haplotype

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10.1093/bioinformatics/btaa729

Cite this

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title = "HaploGrouper: A generalized approach to haplogroup classification",

abstract = "MOTIVATION: We introduce HaploGrouper, a versatile software to classify haplotypes into haplogroups on the basis of a known phylogenetic tree. A typical use case for this software is the assignment of haplogroups to human mitochondrial DNA (mtDNA) or Y-chromosome haplotypes. Existing state-of-the-art haplogroup-calling software is typically hard-wired to work only with either mtDNA or Y-chromosome haplotypes from humans.RESULTS: HaploGrouper exhibits comparable accuracy in these instances and has the advantage of being able to assign haplogroups to any kind of haplotypes from any species-given an extant annotated phylogenetic tree defined by sequence variants.AVAILABILITY AND IMPLEMENTATION: The software is available at the following URL https://gitlab.com/bio\_anth\_decode/haploGrouper.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.",

keywords = "Genes, Haplotype",

author = "Anuradha Jagadeesan and Ebenesersd{\'o}ttir, \{Sigr{\'i}{\dh}ur Sunna\} and Gu{\dh}mundsd{\'o}ttir, \{Vald{\'i}s Bj{\"o}rt\} and Thordardottir, \{Elisabet Linda\} and Moore, \{Kristjan Helgi Swerford\} and Helgason, \{Agnar Sturla\}",

year = "2021",

month = may,

day = "1",

doi = "10.1093/bioinformatics/btaa729",

language = "English",

volume = "37",

pages = "570--572",

journal = "Bioinformatics",

issn = "1367-4803",

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T1 - HaploGrouper

T2 - A generalized approach to haplogroup classification

AU - Jagadeesan, Anuradha

AU - Ebenesersdóttir, Sigríður Sunna

AU - Guðmundsdóttir, Valdís Björt

AU - Thordardottir, Elisabet Linda

AU - Moore, Kristjan Helgi Swerford

AU - Helgason, Agnar Sturla

PY - 2021/5/1

Y1 - 2021/5/1

N2 - MOTIVATION: We introduce HaploGrouper, a versatile software to classify haplotypes into haplogroups on the basis of a known phylogenetic tree. A typical use case for this software is the assignment of haplogroups to human mitochondrial DNA (mtDNA) or Y-chromosome haplotypes. Existing state-of-the-art haplogroup-calling software is typically hard-wired to work only with either mtDNA or Y-chromosome haplotypes from humans.RESULTS: HaploGrouper exhibits comparable accuracy in these instances and has the advantage of being able to assign haplogroups to any kind of haplotypes from any species-given an extant annotated phylogenetic tree defined by sequence variants.AVAILABILITY AND IMPLEMENTATION: The software is available at the following URL https://gitlab.com/bio_anth_decode/haploGrouper.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AB - MOTIVATION: We introduce HaploGrouper, a versatile software to classify haplotypes into haplogroups on the basis of a known phylogenetic tree. A typical use case for this software is the assignment of haplogroups to human mitochondrial DNA (mtDNA) or Y-chromosome haplotypes. Existing state-of-the-art haplogroup-calling software is typically hard-wired to work only with either mtDNA or Y-chromosome haplotypes from humans.RESULTS: HaploGrouper exhibits comparable accuracy in these instances and has the advantage of being able to assign haplogroups to any kind of haplotypes from any species-given an extant annotated phylogenetic tree defined by sequence variants.AVAILABILITY AND IMPLEMENTATION: The software is available at the following URL https://gitlab.com/bio_anth_decode/haploGrouper.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

KW - Genes

KW - Haplotype

UR - https://www.scopus.com/pages/publications/85106069001

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DO - 10.1093/bioinformatics/btaa729

M3 - Article

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SN - 1367-4803

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SP - 570

EP - 572

JO - Bioinformatics

JF - Bioinformatics

IS - 4

ER -

HaploGrouper: A generalized approach to haplogroup classification

Abstract

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