7. Iterative methods

To overcome the dependence on the initial alignment by repeatedly performing the MSA, estimating the value of some heruristic and correcting the previous alignment until convergence is reached.

Global alignment:

  1. Simple iterative method: MulAlin, PRRP, DIALIGN programs
  2. Genetic algorithms (population of MSAs, mutation and recombination events, selection)
  3. Hidden Markov Models

Local alignment (pattern discovery):

  1. Expectation-maximization
  2. Gibbs sampling