Data for article: Generation of accurate, expandable phylogenomic trees with uDANCE

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 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.
Simulated datasets: HD-100, HD-500, MD-100, MD-500, LD-100, HD-P1, HD-P2, HD-P3, HD-P4, HD-P5, HD-HET, Serial, and Varying Backbone size/Partition size/Backbone Tree. Biological datasets: Input, intermediate, and output files for uDance runs that generated the 16K and 200K trees of life.