In simple cases, examples of these two methods can look very similar. Both methods are computationally intense for any but the smallest sets of species. In most real cases, not all characters suggest the same phylogeny. Homoplasy and symplesiomorphy are both common. In practice, the job of reconstructing phylogeny is largely one of distinguishing true synapomorphy from homoplasy.
Homologies are more reliable for phylogenetic inference than are analogies.
This section contains painfully circular reasoning, beginning with the section heading itself. However, the underlying concept is sound. Once phylogeny is known with some confidence, one can determine which similarities are homologous and which are analogous. And one can then see how misleading the analogies might be. The next section suggests tools for breaking out of the circle.