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Comparisons of gene trees and species trees are key to understanding major processes of genome evolution such as gene duplication and loss. Because current methods to reconstruct phylogenies fail to model the two-way dependency between gene trees and the species tree, they often misrepresent gene and species histories. We present a new probabilistic model to jointly infer rooted species and gene trees for dozens of genomes and thousands of gene families. We use simulations to show that thisdoi:10.1101/gr.141978.112 pmid:23132911 pmcid:PMC3561873 fatcat:laidehu2tzabvahk54rcp57v4a