Multiple Sequence Alignment - Use in Phylogenetics

Use in Phylogenetics

Multiple sequence alignments can be used to create a phylogenetic tree. This is made possible by two reasons. The first is because functional domains that are known in annotated sequences can be used for alignment in non-annotated sequences. The other is that conserved regions known to be functionally important can be found. This makes it possible for multiple sequence alignments to be used to analyze and find evolutionary relationships through homology between sequences. Point mutations and insertion or deletion events (called indels) can be detected.

Multiple sequence alignments can also be used to identify functionally important sites, such as binding sites, active sites, or sites corresponding to other key functions, by locating conserved domains. When looking at multiple sequence alignments, it is useful to consider different aspects of the sequences when comparing sequences. These aspects include identity, similarity, and homology. Identity means that the sequences have identical residues at their respective positions. On the other hand, similarity has to do with the sequences being compared having similar residues quantitatively. For example, in terms of nucleotide sequences, pyrimidines are considered similar to each other, as are purines. Similarity ultimately leads to homology, in that the more similar sequences are, the closer they are to being homologous. This similarity in sequences can then go on to help find common ancestry.