Complications to phylogenetic analysis

The process of generating phylogenetic trees as described so far is straightforward - this is a gross simplification. Phylogenetic analysis is an entire scientific area of study, and of course whats been presented is very highly simplified. In this section, we'll touch (just touch) on some of the refinements that are often considered in more sophisticated analyses:

In some cases, however, ssu-rRNA analysis just doesn't have the resolution required. Generally speaking, ssu-rRNA analysis cannot be used to identify organisms more specifically than at the genus - not the species. Some alternative approaches are: