Biological sequences come in families

• most powerful sequence analysis methods are the ones which try to model the relationship of an individual sequence to a sequence family
• sequences within a family might have changed from a base sequence during evolution and the diffeerences could be due to
  • duplication in the genome
  • speciation
• yet they will have similar function

If we know some sequences belonging to a family, for a new query sequence we can directly try to get the distance score through pairwise searching.

• you can search with either one sample from the family or

• all the sequences in the family

• Rather than this sort of method, a better one would be to look at the statistical features of all the sequences