Generation of accurate, expandable phylogenomic trees with uDance.

Autor: Balaban, Metin, Jiang, Yueyu, Zhu, Qiyun, McDonald, Daniel, Knight, Rob, Mirarab, Siavash
Zdroj: Nature Biotechnology; May2024, Vol. 42 Issue 5, p768-777, 10p
Abstrakt: 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. Large, updatable phylogenetic trees are constructed using a divide-and-conquer strategy. [ABSTRACT FROM AUTHOR]
Databáze: Complementary Index
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