Birds are an extensively studied clade with more than 10,000 named species. Many relationships within birds have proven to be difficult to recover in phylogenetic analyses. This difficulty reflects several factors, including discordance among gene trees, shifts in evolutionary rates, changes in the model of sequence evolution across the avian tree, and the complexity of the recombination landscape for bird genomes. There are multiple efforts to generate sequence data for all bird taxa; this talk will focus on an effort to use ultraconserved element (UCE) sequence capture to generate data for all currently recognized bird species. Analyses of UCE data for large numbers of taxa presents several challenges. More specifically, I will describe the performance of phylogenomic methods with a UCE dataset with hundreds and thousands of taxa. The methods used in these comparisons include the commonly used methods (maximum likelihood analysis of concatenated data, gene tree summary methods, and SVDquartets) as well as a “new” method called METAL (Metric algorithm for Estimation of Trees based on Aggregation of Loci). Empirical studies have obvious limitations since they represent a single realization of an evolutionary history, but they also provide information that is difficult to obtain in more controlled situations like simulations.