ArticleBMC genomics2013
AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- UYSD: a novel data repository accessible via public website for worldwide population frequencies of Y-SNP haplogroups.European journal of human genetics : EJHG · 2025Article
- Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data.Computational and structural biotechnology journal · 2023Article
- Ancestry-related distribution of Runs of homozygosity and functional variants in Qatari population.BMC genomic data · 2022Article
- Genetic substructure and complex demographic history of South African Bantu speakers.Nature communications · 2021Article
- Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data.BMC bioinformatics · 2021Article
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- Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences.Genome biology and evolution · 2020Article
- Introducing the first whole genomes of nationals from the United Arab Emirates.Scientific reports · 2019Article
- Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations.Genome biology · 2019Article
- Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia.Nature genetics · 2018Article
- Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans.Nature communications · 2017Article
- Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81).Scientific reports · 2017Article
- Next Generation Sequencing Plus (NGS+) with Y-chromosomal Markers for Forensic Pedigree Searches.Scientific reports · 2017Article
- Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Large-scale recent expansion of European patrilineages shown by population resequencing.Nature communications · 2015Article
- The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades.Molecular biology and evolution · 2015Article
- Kuwaiti population subgroup of nomadic Bedouin ancestry-Whole genome sequence and analysis.Genomics data · 2015Article
- Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry.BMC genomics · 2015Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundDue to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase the resolution of the phylogenetic Y chromosomal tree. Moreover, the exponential growth of known Y chromosomal lineages will require an automatic determination of the phylogenetic position of an individual based on whole genome SNP calling data and an up to date Y chromosomal tree.
resultsWe present an automated approach, 'AMY-tree', which is able to determine the phylogenetic position of a Y chromosome using a whole genome SNP profile, independently from the NGS platform and SNP calling program, whereby mistakes in the SNP calling or phylogenetic Y chromosomal tree are taken into account. Moreover, AMY-tree indicates ambiguities within the present phylogenetic tree and points out new Y-SNPs which may be phylogenetically relevant. The AMY-tree software package was validated successfully on 118 whole genome SNP profiles of 109 males with different origins. Moreover, support was found for an unknown recurrent mutation, wrong reported mutation conversions and a large amount of new interesting Y-SNPs.
conclusionsTherefore, AMY-tree is a useful tool to determine the Y lineage of a sample based on SNP calling, to identify Y-SNPs with yet unknown phylogenetic position and to optimize the Y chromosomal phylogenetic tree in the future. AMY-tree will not add lineages to the existing phylogenetic tree of the Y-chromosome but it is the first step to analyse whole genome SNP profiles in a phylogenetic framework.
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