4. Multiple alignment and molecular phylogeny

Here we leave the realm of isolated sequence analysis, and enter the world of multiple comparisons.

While the sequence alignment methods mentioned in the previous paragraphs have, until now, only taken advantage of similarity information, the approaches presented will now attempt to interpret their differences or, at the very least, the contrast between their differences and similarities.

While alignment methods are all the more effective the closer the sequences compared, those presented here will be all the more informative the more divergent the sequences used, although still homologous.