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

Access to Document

10.1093/bioinformatics/btaa729

Cite this

@article{f9a9c2ae918f4556a226d932cbce928a,

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",

publisher = "Oxford University Press",

number = "4",

}

TY - JOUR

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

U2 - 10.1093/bioinformatics/btaa729

DO - 10.1093/bioinformatics/btaa729

M3 - Article

C2 - 32805011

SN - 1367-4803

VL - 37

SP - 570

EP - 572

JO - Bioinformatics

JF - Bioinformatics

IS - 4

ER -

HaploGrouper: A generalized approach to haplogroup classification

Abstract

Bibliographical note

Other keywords

Access to Document

Fingerprint

Cite this