These datasets test the ability of SPIDIR and other phylogenetic methods to recover the correct gene tree. In real datasets, syntenic orthologs are used. With one-to-one syntenic orthologs, correctness is defined as congruent to species tree. For whole genome duplicated orthologs and paralogs, correctness is defined by placing paralogs on opposing sides of the whole genome duplication event. For simulated datasets, various other duplication and loss scenarios are tested.
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Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
Matthew D. Rasmussen and Manolis Kellis.
Genome Res. 2007. 17: 1932-1942