ABSTRACT
The long-term trend in phylogenomics has been a reduction in time for amassing sequence data, which has had the favorable consequence of allowing researchers more time to conduct analyses. A. Rokas et al. conducted a completely in silico phylogenomic study involving eight species of yeasts whose genomes had already been sequenced. For a phylogenomic study, the high costs of genomes means that a tradeoff exists between the numbers of genomes that can be sequenced versus numbers of species that can be sampled. E. D. Jarvis et al. used computer-based methods to construct datasets based on Ultraconserved elements-anchored loci but their data were derived from genomes that they themselves had earlier sequenced and assembled. The computer-based process of generating deoxyribonucleic acid sequence datasets can be automated from start to finish: software can be used to extract target loci sequences from all sampled genomes, perform multiple sequence alignments, and output ready-to-analyze datasets.
