Sometimes phylogenies are estimated by concatenating genes to create a combined alignment (see references below). Gene subset ensembles can be constructed by selecting different subsets of genes to include in the alignment. This provides another method for assessing whether tree estimation is robust.
Note that each gene should be aligned separately before concatenating into a bigger MSA.
References
Bapteste, Eric, et al. "Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny." Molecular Biology and Evolution 25.1 (2008): 83-91. link
Vitorino, Liliana, et al. "Rickettsiae phylogeny: a multigenic approach." Microbiology 153.1 (2007): 160-168. link
Kubatko, Laura Salter, and James H. Degnan. "Inconsistency of phylogenetic estimates from concatenated data under coalescence." Systematic biology 56.1 (2007): 17-24. link
