[1] The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions.
However, Eisen noted that H. pylori lacks other genes thought to be essential for this function (specifically, members of the MutL family).
Using these methods, researchers were able to identify over 2,000 metabolic enzymes obtained by various eukaryotic parasites from lateral gene transfer.
For example, multiple duplications of genes encoding degradative enzymes of certain families is a common adaptation in microbes to new nutrient sources.
By using entire genomes in these comparisons, the anomalies created from these factors are overwhelmed by the pattern of evolution indicated by the majority of the data.
[11][12][13] Through phylogenomics, it has been discovered that most of the photosynthetic eukaryotes are linked and possibly share a single ancestor.
Using this method, it is theoretically possible to create fully resolved phylogenetic trees, and timing constraints can be recovered more accurately.