TY - JOUR
T1 - Generation of accurate, expandable phylogenomic trees with uDance
AU - Balaban, Metin
AU - Jiang, Yueyu
AU - Zhu, Qiyun
AU - McDonald, Daniel
AU - Knight, Rob
AU - Mirarab, Siavash
N1 - Publisher Copyright:
© 2023, The Author(s), under exclusive licence to Springer Nature America, Inc.
PY - 2023
Y1 - 2023
N2 - Phylogenetic trees provide a framework for organizing evolutionary histories across the tree of life and aid downstream comparative analyses such as metagenomic identification. Methods that rely on single-marker genes such as 16S rRNA have produced trees of limited accuracy with hundreds of thousands of organisms, whereas methods that use genome-wide data are not scalable to large numbers of genomes. We introduce updating trees using divide-and-conquer (uDance), a method that enables updatable genome-wide inference using a divide-and-conquer strategy that refines different parts of the tree independently and can build off of existing trees, with high accuracy and scalability. With uDance, we infer a species tree of roughly 200,000 genomes using 387 marker genes, totaling 42.5 billion amino acid residues.
AB - Phylogenetic trees provide a framework for organizing evolutionary histories across the tree of life and aid downstream comparative analyses such as metagenomic identification. Methods that rely on single-marker genes such as 16S rRNA have produced trees of limited accuracy with hundreds of thousands of organisms, whereas methods that use genome-wide data are not scalable to large numbers of genomes. We introduce updating trees using divide-and-conquer (uDance), a method that enables updatable genome-wide inference using a divide-and-conquer strategy that refines different parts of the tree independently and can build off of existing trees, with high accuracy and scalability. With uDance, we infer a species tree of roughly 200,000 genomes using 387 marker genes, totaling 42.5 billion amino acid residues.
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U2 - 10.1038/s41587-023-01868-8
DO - 10.1038/s41587-023-01868-8
M3 - Article
AN - SCOPUS:85165917040
SN - 1087-0156
JO - Nature biotechnology
JF - Nature biotechnology
ER -