Two-dimensional gel electrophoresis is one of the most powerful resolving methods now available.
Among these studies of genome trees, the alignment-free methods proposed by Gao and Qi [ 1], Wu et al [ 2], Gao et al [ 12] and Stuart et al [ 16] seem to be sufficiently powerful to resolve the phylogeny of viruses at large evolutionary distance.
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This approach is simple in its algorithm but powerful in resolving situations when two datasets have significant coordinate discrepancies.
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GC-MS is powerful for resolving compounds that are volatile or can be volatilized through derivation such as the small molecules of primary central metabolism.
Though gene order approach is powerful in resolving controversial phylogenetic relationships, there are some limitations for the application of gene order to phylogenetic reconstruction of closely related organisms.
Inferelator 1.0 proved particularly powerful at resolving the directionality of regulatory interactions, i.e. "who regulates who" (approximately <img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0009803.e001.PNG" class= inline-graphic"/> of identified true positives were correctly resolved).
Individual mitochondrial genes and nuclear genes seem to be less powerful in resolving phylogenetic relationships within the Galliformes, especially the Phasianidae.
Complete mtDNA sequences provide sets of genome-level characteristics, such as gene rearrangement, which is rather conserved within some major metazoan lineages, and therefore can be especially powerful in resolving systematic relationships among higher taxa [ 3, 40, 42, 47- 49].
Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders.
