The moth midge Clogmia albipunctata [phylome 183], the scuttle fly Megaselia abdita  and the hoverfly Episyrphus balteatus . These phylomes were computed as part of a stuy aiming to characterize the transcriptomes of these three dipteran species that serve as a model to study early dipteran development and its evolution (Jiménez-Guri et. al. 20013). As such this is the first time that the PhylomeDB pipeline was applied to a transcriptome, showing satisfactory results but highlighting the necessity to deal with expected artifacts resulting from the analysis of a direct transcriptome assembly: missing genes, partial sequences, and sometimes failure to combine transcripts from the same gene. A solution that worked was to use an additional species with a complete genome (D. melanogaster in this case [phylome 191]), as a seed for the analyses of these transcriptomes. We used these data to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies).
Comparative transcriptomics of early dipteran development. Jiménez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldón T, Jaeger J. (2013) BMC Genomics. 14(1):123.